R Under development (unstable) (2024-02-16 r85931 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(PSCBS) PSCBS v0.67.0 successfully loaded. See ?PSCBS for help. > library(utils) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Load SNP microarray data > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > data <- PSCBS::exampleData("paired.chr01") > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Paired PSCBS segmentation > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Drop single-locus outliers > dataS <- dropSegmentationOutliers(data) > > # Run light-weight tests by default > if (Sys.getenv("_R_CHECK_FULL_") == "") { + # Use only every 5th data point + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] + # Number of segments (for assertion) + nSegs <- 4L + } else { + # Full tests + nSegs <- 11L + } > > str(dataS) 'data.frame': 14670 obs. of 6 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... $ CT : num 1.63 1.4 1.41 1.17 1.16 ... $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... $ CN : num 2.36 2.13 2.26 2.01 2.32 ... $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... > > > ## Create multiple chromosomes > data <- list() > for (cc in 1:3) { + dataS$chromosome <- cc + data[[cc]] <- dataS + } > data <- Reduce(rbind, data) > str(data) 'data.frame': 44010 obs. of 6 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... $ CT : num 1.63 1.4 1.41 1.17 1.16 ... $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... $ CN : num 2.36 2.13 2.26 2.01 2.32 ... $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... > > > message("*** segmentByPairedPSCBS() via futures ...") *** segmentByPairedPSCBS() via futures ... > > library("future") > oplan <- plan() > > strategies <- c("sequential", "multisession") > > ## Test 'future.batchtools' futures? > pkg <- "future.batchtools" > if (require(pkg, character.only=TRUE)) { + strategies <- c(strategies, "batchtools_local") + } Loading required package: future.batchtools Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'future.batchtools' > > message("Future strategies to test: ", paste(sQuote(strategies), collapse=", ")) Future strategies to test: 'sequential', 'multisession' > > fits <- list() > for (strategy in strategies) { + message(sprintf("- segmentByPairedPSCBS() using '%s' futures ...", strategy)) + plan(strategy) + fit <- segmentByPairedPSCBS(data, seed=0xBEEF, verbose=TRUE) + fits[[strategy]] <- fit + equal <- all.equal(fit, fits[[1]]) + if (!equal) { + str(fit) + str(fits[[1]]) + print(equal) + stop(sprintf("segmentByPairedPSCBS() using '%s' futures does not produce the same results as when using '%s' futures", strategy, names(fits)[1])) + } + } - segmentByPairedPSCBS() using 'sequential' futures ... Segmenting paired tumor-normal signals using Paired PSCBS... Calling genotypes from normal allele B fractions... num [1:44010] 0.8274 0.5072 0.1671 0.1609 0.0421 ... Called genotypes: num [1:44010] 1 0.5 0 0 0 0 1 0 1 0.5 ... - attr(*, "modelFit")=List of 1 ..$ :List of 7 .. ..$ flavor : chr "density" .. ..$ cn : int 2 .. ..$ nbrOfGenotypeGroups: int 3 .. ..$ tau : num [1:2] 0.312 0.678 .. ..$ n : int 43920 .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. ..$ type : chr [1:2] "valley" "valley" .. .. ..$ x : num [1:2] 0.312 0.678 .. .. ..$ density: num [1:2] 0.465 0.496 ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" muN 0 0.5 1 15627 12633 15750 Calling genotypes from normal allele B fractions...done Normalizing betaT using betaN (TumorBoost)... Normalized BAFs: num [1:44010] 0.9301 0.1667 0.0685 0.0995 0.0155 ... - attr(*, "modelFit")=List of 5 ..$ method : chr "normalizeTumorBoost" ..$ flavor : chr "v4" ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. ..- attr(*, "modelFit")=List of 1 .. .. ..$ :List of 7 .. .. .. ..$ flavor : chr "density" .. .. .. ..$ cn : int 2 .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. ..$ tau : num [1:2] 0.312 0.678 .. .. .. ..$ n : int 43920 .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. ..$ x : num [1:2] 0.312 0.678 .. .. .. .. ..$ density: num [1:2] 0.465 0.496 .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" ..$ preserveScale: logi FALSE ..$ scaleFactor : num NA Normalizing betaT using betaN (TumorBoost)...done Setup up data... 'data.frame': 44010 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1145994 2941694 3710825 4240737 4276892 ... $ CT : num 1.63 1.4 1.41 1.17 1.16 ... $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... ..- attr(*, "modelFit")=List of 5 .. ..$ method : chr "normalizeTumorBoost" .. ..$ flavor : chr "v4" .. ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. .. ..- attr(*, "modelFit")=List of 1 .. .. .. ..$ :List of 7 .. .. .. .. ..$ flavor : chr "density" .. .. .. .. ..$ cn : int 2 .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. .. ..$ tau : num [1:2] 0.312 0.678 .. .. .. .. ..$ n : int 43920 .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. .. .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. .. ..$ x : num [1:2] 0.312 0.678 .. .. .. .. .. ..$ density: num [1:2] 0.465 0.496 .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" .. ..$ preserveScale: logi FALSE .. ..$ scaleFactor : num NA $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... ..- attr(*, "modelFit")=List of 1 .. ..$ :List of 7 .. .. ..$ flavor : chr "density" .. .. ..$ cn : int 2 .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. ..$ tau : num [1:2] 0.312 0.678 .. .. ..$ n : int 43920 .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. ..$ x : num [1:2] 0.312 0.678 .. .. .. ..$ density: num [1:2] 0.465 0.496 .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" Setup up data...done Dropping loci for which TCNs are missing... Number of loci dropped: 36 Dropping loci for which TCNs are missing...done Ordering data along genome... 'data.frame': 43974 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Segmenting multiple chromosomes... Number of chromosomes: 3 Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") Produced 3 seeds from this stream for future usage Chromosome #1 ('Chr01') of 3... 'data.frame': 14658 obs. of 8 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... Known segments: [1] chromosome start end <0 rows> (or 0-length row.names) Segmenting paired tumor-normal signals using Paired PSCBS... Setup up data... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Setup up data...done Ordering data along genome... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Keeping only current chromosome for 'knownSegments'... Chromosome: 1 Known segments for this chromosome: [1] chromosome start end <0 rows> (or 0-length row.names) Keeping only current chromosome for 'knownSegments'...done alphaTCN: 0.009 alphaDH: 0.001 Number of loci: 14658 Calculating DHs... Number of SNPs: 14658 Number of heterozygous SNPs: 4209 (28.71%) Normalized DHs: num [1:14658] NA NA NA NA NA ... Calculating DHs...done Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") Produced 2 seeds from this stream for future usage Identification of change points by total copy numbers... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 3 obs. of 6 variables: ..$ sampleName: chr [1:3] NA NA NA ..$ chromosome: int [1:3] 1 1 1 ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:3] 7599 2668 4391 ..$ mean : num [1:3] 1.39 2.07 2.63 $ segRows:'data.frame': 3 obs. of 2 variables: ..$ startRow: int [1:3] 1 7600 10268 ..$ endRow : int [1:3] 7599 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num -Inf .. ..$ end : num Inf ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.58 0 0.57 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 1 554484 143926517 7599 1.3859 2 1 143926517 185449813 2668 2.0704 3 1 185449813 247137334 4391 2.6341 Number of TCN segments: 3 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.43927e+08]) of 3... Number of TCN loci in segment: 7599 Locus data for TCN segment: 'data.frame': 7599 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7599 Number of SNPs: 2120 (27.90%) Number of heterozygous SNPs: 2120 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7599 obs. of 4 variables: ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7599] NA NA NA NA NA ... ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 554484 ..$ end : num 1.44e+08 ..$ nbrOfLoci : int 2120 ..$ mean : num 0.51 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7594 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 554484 .. ..$ end : num 1.44e+08 ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.06 0 0.06 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7594 int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7594 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 143926517 2120 0.5101 startRow endRow 1 10 7594 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 startRow endRow 1 10 7594 NULL TCN segmentation (expanded) rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 startRow endRow 1 1 7599 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 1 554484 143926517 7599 1.3859 2120 2120 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... Number of TCN loci in segment: 2668 Locus data for TCN segment: 'data.frame': 2668 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... $ CT : num 2.1 2.1 2.09 1.8 2.34 ... $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... $ muN : num 0 1 1 0 0 1 0 0 0 0 ... $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... $ rho : num NA NA NA NA NA NA NA NA NA NA ... Number of loci: 2668 Number of SNPs: 775 (29.05%) Number of heterozygous SNPs: 775 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 2668 obs. of 4 variables: ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.44e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 775 ..$ mean : num 0.097 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 15 ..$ endRow : int 2664 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.44e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 DH segmentation (locally-indexed) rows: startRow endRow 1 15 2664 int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... DH segmentation rows: startRow endRow 1 7614 10263 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 143926517 185449813 775 0.097 startRow endRow 1 7614 10263 Rows: [1] 2 TCN segmentation rows: startRow endRow 2 7600 10267 TCN and DH segmentation rows: startRow endRow 2 7600 10267 startRow endRow 1 7614 10263 startRow endRow 1 1 7599 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 startRow endRow 1 1 7599 2 7600 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 1 143926517 185449813 2668 2.0704 775 775 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 1 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 775 143926517 185449813 775 0.097 Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1314 (29.92%) Number of heterozygous SNPs: 1314 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1314 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.03 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 DH segmentation (locally-indexed) rows: startRow endRow 1 2 4388 int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1314 0.2295 startRow endRow 1 10269 14655 Rows: [1] 3 TCN segmentation rows: startRow endRow 3 10268 14658 TCN and DH segmentation rows: startRow endRow 3 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7599 2 7600 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 3 10269 14655 startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 1 185449813 247137334 4391 2.6341 1314 1314 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 1314 185449813 247137334 1314 0.2295 Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 2 775 143926517 185449813 775 0.0970 3 1314 185449813 247137334 1314 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 3 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 3 Number of chromosomes: 1 [1] 1 Chromosome 1 ('chr01') of 1... Rows: [1] 1 2 3 Number of segments: 3 TCN segment #1 ('1') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 3...done TCN segment #2 ('2') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 3...done TCN segment #3 ('3') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #3 ('3') of 3...done Chromosome 1 ('chr01') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 Chromosome #1 ('Chr01') of 3...done Chromosome #2 ('Chr02') of 3... 'data.frame': 14658 obs. of 8 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 14659 14660 14661 14662 14663 14664 14665 14666 14667 14668 ... Known segments: [1] chromosome start end <0 rows> (or 0-length row.names) Segmenting paired tumor-normal signals using Paired PSCBS... Setup up data... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Setup up data...done Ordering data along genome... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Keeping only current chromosome for 'knownSegments'... Chromosome: 2 Known segments for this chromosome: [1] chromosome start end <0 rows> (or 0-length row.names) Keeping only current chromosome for 'knownSegments'...done alphaTCN: 0.009 alphaDH: 0.001 Number of loci: 14658 Calculating DHs... Number of SNPs: 14658 Number of heterozygous SNPs: 4209 (28.71%) Normalized DHs: num [1:14658] NA NA NA NA NA ... Calculating DHs...done Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Produced 2 seeds from this stream for future usage Identification of change points by total copy numbers... Segmenting by CBS... Chromosome: 2 Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 3 obs. of 6 variables: ..$ sampleName: chr [1:3] NA NA NA ..$ chromosome: int [1:3] 2 2 2 ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:3] 7599 2668 4391 ..$ mean : num [1:3] 1.39 2.07 2.63 $ segRows:'data.frame': 3 obs. of 2 variables: ..$ startRow: int [1:3] 1 7600 10268 ..$ endRow : int [1:3] 7599 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num -Inf .. ..$ end : num Inf ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.45 0 0.45 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 2 554484 143926517 7599 1.3859 2 2 143926517 185449813 2668 2.0704 3 2 185449813 247137334 4391 2.6341 Number of TCN segments: 3 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.43927e+08]) of 3... Number of TCN loci in segment: 7599 Locus data for TCN segment: 'data.frame': 7599 obs. of 9 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7599 Number of SNPs: 2120 (27.90%) Number of heterozygous SNPs: 2120 (100.00%) Chromosome: 2 Segmenting DH signals... Segmenting by CBS... Chromosome: 2 Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7599 obs. of 4 variables: ..$ chromosome: int [1:7599] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7599] NA NA NA NA NA ... ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 2 ..$ start : num 554484 ..$ end : num 1.44e+08 ..$ nbrOfLoci : int 2120 ..$ mean : num 0.51 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7594 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num 554484 .. ..$ end : num 1.44e+08 ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.03 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7594 int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7594 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 143926517 2120 0.5101 startRow endRow 1 10 7594 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 startRow endRow 1 10 7594 NULL TCN segmentation (expanded) rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 startRow endRow 1 1 7599 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 2 554484 143926517 7599 1.3859 2120 2120 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 2 554484 143926517 7599 1.3859 2120 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... Number of TCN loci in segment: 2668 Locus data for TCN segment: 'data.frame': 2668 obs. of 9 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... $ CT : num 2.1 2.1 2.09 1.8 2.34 ... $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... $ muN : num 0 1 1 0 0 1 0 0 0 0 ... $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... $ rho : num NA NA NA NA NA NA NA NA NA NA ... Number of loci: 2668 Number of SNPs: 775 (29.05%) Number of heterozygous SNPs: 775 (100.00%) Chromosome: 2 Segmenting DH signals... Segmenting by CBS... Chromosome: 2 Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 2668 obs. of 4 variables: ..$ chromosome: int [1:2668] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 2 ..$ start : num 1.44e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 775 ..$ mean : num 0.097 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 15 ..$ endRow : int 2664 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num 1.44e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.01 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 DH segmentation (locally-indexed) rows: startRow endRow 1 15 2664 int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... DH segmentation rows: startRow endRow 1 7614 10263 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 143926517 185449813 775 0.097 startRow endRow 1 7614 10263 Rows: [1] 2 TCN segmentation rows: startRow endRow 2 7600 10267 TCN and DH segmentation rows: startRow endRow 2 7600 10267 startRow endRow 1 7614 10263 startRow endRow 1 1 7599 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 startRow endRow 1 1 7599 2 7600 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 2 143926517 185449813 2668 2.0704 775 775 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 2 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 775 143926517 185449813 775 0.097 Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1314 (29.92%) Number of heterozygous SNPs: 1314 (100.00%) Chromosome: 2 Segmenting DH signals... Segmenting by CBS... Chromosome: 2 Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 2 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1314 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.03 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 DH segmentation (locally-indexed) rows: startRow endRow 1 2 4388 int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1314 0.2295 startRow endRow 1 10269 14655 Rows: [1] 3 TCN segmentation rows: startRow endRow 3 10268 14658 TCN and DH segmentation rows: startRow endRow 3 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7599 2 7600 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 3 10269 14655 startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 2 185449813 247137334 4391 2.6341 1314 1314 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 2 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 1314 185449813 247137334 1314 0.2295 Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 2 775 143926517 185449813 775 0.0970 3 1314 185449813 247137334 1314 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 3 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 3 Number of chromosomes: 1 [1] 2 Chromosome 1 ('chr02') of 1... Rows: [1] 1 2 3 Number of segments: 3 TCN segment #1 ('1') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 3...done TCN segment #2 ('2') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 3...done TCN segment #3 ('3') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #3 ('3') of 3...done Chromosome 1 ('chr02') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 Chromosome #2 ('Chr02') of 3...done Chromosome #3 ('Chr03') of 3... 'data.frame': 14658 obs. of 8 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 29317 29318 29319 29320 29321 29322 29323 29324 29325 29326 ... Known segments: [1] chromosome start end <0 rows> (or 0-length row.names) Segmenting paired tumor-normal signals using Paired PSCBS... Setup up data... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Setup up data...done Ordering data along genome... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Keeping only current chromosome for 'knownSegments'... Chromosome: 3 Known segments for this chromosome: [1] chromosome start end <0 rows> (or 0-length row.names) Keeping only current chromosome for 'knownSegments'...done alphaTCN: 0.009 alphaDH: 0.001 Number of loci: 14658 Calculating DHs... Number of SNPs: 14658 Number of heterozygous SNPs: 4209 (28.71%) Normalized DHs: num [1:14658] NA NA NA NA NA ... Calculating DHs...done Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Produced 2 seeds from this stream for future usage Identification of change points by total copy numbers... Segmenting by CBS... Chromosome: 3 Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 3 obs. of 6 variables: ..$ sampleName: chr [1:3] NA NA NA ..$ chromosome: int [1:3] 3 3 3 ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:3] 7599 2668 4391 ..$ mean : num [1:3] 1.39 2.07 2.63 $ segRows:'data.frame': 3 obs. of 2 variables: ..$ startRow: int [1:3] 1 7600 10268 ..$ endRow : int [1:3] 7599 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num -Inf .. ..$ end : num Inf ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.41 0 0.41 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 3 554484 143926517 7599 1.3859 2 3 143926517 185449813 2668 2.0704 3 3 185449813 247137334 4391 2.6341 Number of TCN segments: 3 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.43927e+08]) of 3... Number of TCN loci in segment: 7599 Locus data for TCN segment: 'data.frame': 7599 obs. of 9 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7599 Number of SNPs: 2120 (27.90%) Number of heterozygous SNPs: 2120 (100.00%) Chromosome: 3 Segmenting DH signals... Segmenting by CBS... Chromosome: 3 Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7599 obs. of 4 variables: ..$ chromosome: int [1:7599] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7599] NA NA NA NA NA ... ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 3 ..$ start : num 554484 ..$ end : num 1.44e+08 ..$ nbrOfLoci : int 2120 ..$ mean : num 0.51 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7594 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num 554484 .. ..$ end : num 1.44e+08 ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.03 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7594 int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7594 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 143926517 2120 0.5101 startRow endRow 1 10 7594 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 startRow endRow 1 10 7594 NULL TCN segmentation (expanded) rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 startRow endRow 1 1 7599 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 3 554484 143926517 7599 1.3859 2120 2120 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 3 554484 143926517 7599 1.3859 2120 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... Number of TCN loci in segment: 2668 Locus data for TCN segment: 'data.frame': 2668 obs. of 9 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... $ CT : num 2.1 2.1 2.09 1.8 2.34 ... $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... $ muN : num 0 1 1 0 0 1 0 0 0 0 ... $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... $ rho : num NA NA NA NA NA NA NA NA NA NA ... Number of loci: 2668 Number of SNPs: 775 (29.05%) Number of heterozygous SNPs: 775 (100.00%) Chromosome: 3 Segmenting DH signals... Segmenting by CBS... Chromosome: 3 Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 2668 obs. of 4 variables: ..$ chromosome: int [1:2668] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 3 ..$ start : num 1.44e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 775 ..$ mean : num 0.097 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 15 ..$ endRow : int 2664 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num 1.44e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0 0 0 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 DH segmentation (locally-indexed) rows: startRow endRow 1 15 2664 int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... DH segmentation rows: startRow endRow 1 7614 10263 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 143926517 185449813 775 0.097 startRow endRow 1 7614 10263 Rows: [1] 2 TCN segmentation rows: startRow endRow 2 7600 10267 TCN and DH segmentation rows: startRow endRow 2 7600 10267 startRow endRow 1 7614 10263 startRow endRow 1 1 7599 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 startRow endRow 1 1 7599 2 7600 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 3 143926517 185449813 2668 2.0704 775 775 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 3 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 775 143926517 185449813 775 0.097 Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1314 (29.92%) Number of heterozygous SNPs: 1314 (100.00%) Chromosome: 3 Segmenting DH signals... Segmenting by CBS... Chromosome: 3 Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 3 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1314 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.01 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 DH segmentation (locally-indexed) rows: startRow endRow 1 2 4388 int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1314 0.2295 startRow endRow 1 10269 14655 Rows: [1] 3 TCN segmentation rows: startRow endRow 3 10268 14658 TCN and DH segmentation rows: startRow endRow 3 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7599 2 7600 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 3 10269 14655 startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 3 185449813 247137334 4391 2.6341 1314 1314 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 3 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 1314 185449813 247137334 1314 0.2295 Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 2 775 143926517 185449813 775 0.0970 3 1314 185449813 247137334 1314 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 3 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 3 Number of chromosomes: 1 [1] 3 Chromosome 1 ('chr03') of 1... Rows: [1] 1 2 3 Number of segments: 3 TCN segment #1 ('1') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 3...done TCN segment #2 ('2') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 3...done TCN segment #3 ('3') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #3 ('3') of 3...done Chromosome 1 ('chr03') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 Chromosome #3 ('Chr03') of 3...done Merging (independently) segmented chromosome... List of 5 $ data :Classes 'PairedPSCNData' and 'data.frame': 43974 obs. of 8 variables: ..$ chromosome: int [1:43974] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:43974] 554484 730720 782343 878522 916294 ... ..$ CT : num [1:43974] 1.88 1.8 1.59 1.64 1.53 ... ..$ betaT : num [1:43974] 0.0646 0.1672 0.9284 0.113 0.7209 ... ..$ betaTN : num [1:43974] -0.0515 -0.1172 1.0194 0.031 0.8604 ... ..$ betaN : num [1:43974] 0.116 0.284 0.909 0.082 0.86 ... ..$ muN : num [1:43974] 0 0 1 0 1 1 1 0 1 0.5 ... ..$ rho : num [1:43974] NA NA NA NA NA ... $ output :Classes 'PairedPSCNSegments' and 'data.frame': 11 obs. of 15 variables: ..$ chromosome : int [1:11] 1 1 1 NA 2 2 2 NA 3 3 ... ..$ tcnId : int [1:11] 1 2 3 NA 1 2 3 NA 1 2 ... ..$ dhId : int [1:11] 1 1 1 NA 1 1 1 NA 1 1 ... ..$ tcnStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... ..$ tcnEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... ..$ tcnNbrOfLoci: int [1:11] 7599 2668 4391 NA 7599 2668 4391 NA 7599 2668 ... ..$ tcnMean : num [1:11] 1.39 2.07 2.63 NA 1.39 ... ..$ tcnNbrOfSNPs: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... ..$ tcnNbrOfHets: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... ..$ dhStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... ..$ dhEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... ..$ dhNbrOfLoci : int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... ..$ dhMean : num [1:11] 0.51 0.097 0.23 NA 0.51 ... ..$ c1Mean : num [1:11] 0.339 0.935 1.015 NA 0.339 ... ..$ c2Mean : num [1:11] 1.05 1.14 1.62 NA 1.05 ... $ tcnSegRows:'data.frame': 11 obs. of 2 variables: ..$ startRow: int [1:11] 1 7600 10268 NA 14659 22258 24926 NA 29317 36916 ... ..$ endRow : int [1:11] 7599 10267 14658 NA 22257 24925 29316 NA 36915 39583 ... $ dhSegRows :'data.frame': 11 obs. of 2 variables: ..$ startRow: int [1:11] 10 7614 10269 NA 14668 22272 24927 NA 29326 36930 ... ..$ endRow : int [1:11] 7594 10263 14655 NA 22252 24921 29313 NA 36910 39579 ... $ params :List of 7 ..$ alphaTCN : num 0.009 ..$ alphaDH : num 0.001 ..$ flavor : chr "tcn&dh" ..$ tbn : logi FALSE ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 0 obs. of 3 variables: .. ..$ chromosome: int(0) .. ..$ start : int(0) .. ..$ end : int(0) ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" Merging (independently) segmented chromosome...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 4 NA NA NA NA NA NA NA NA 5 2 1 1 554484 143926517 7599 1.3859 2120 6 2 2 1 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 4 NA NA NA NA NA NA NA 5 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 6 2 2 1 143926517 185449813 2668 2.0704 775 7 2 3 1 185449813 247137334 4391 2.6341 1314 8 NA NA NA NA NA NA NA NA 9 3 1 1 554484 143926517 7599 1.3859 2120 10 3 2 1 143926517 185449813 2668 2.0704 775 11 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 7 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 8 NA NA NA NA NA NA NA 9 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 10 775 143926517 185449813 775 0.0970 0.9347856 1.135614 11 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 Segmenting multiple chromosomes...done Segmenting paired tumor-normal signals using Paired PSCBS...done - segmentByPairedPSCBS() using 'multisession' futures ... Segmenting paired tumor-normal signals using Paired PSCBS... Calling genotypes from normal allele B fractions... num [1:44010] 0.8274 0.5072 0.1671 0.1609 0.0421 ... Called genotypes: num [1:44010] 1 0.5 0 0 0 0 1 0 1 0.5 ... - attr(*, "modelFit")=List of 1 ..$ :List of 7 .. ..$ flavor : chr "density" .. ..$ cn : int 2 .. ..$ nbrOfGenotypeGroups: int 3 .. ..$ tau : num [1:2] 0.312 0.678 .. ..$ n : int 43920 .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. ..$ type : chr [1:2] "valley" "valley" .. .. ..$ x : num [1:2] 0.312 0.678 .. .. ..$ density: num [1:2] 0.465 0.496 ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" muN 0 0.5 1 15627 12633 15750 Calling genotypes from normal allele B fractions...done Normalizing betaT using betaN (TumorBoost)... Normalized BAFs: num [1:44010] 0.9301 0.1667 0.0685 0.0995 0.0155 ... - attr(*, "modelFit")=List of 5 ..$ method : chr "normalizeTumorBoost" ..$ flavor : chr "v4" ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. ..- attr(*, "modelFit")=List of 1 .. .. ..$ :List of 7 .. .. .. ..$ flavor : chr "density" .. .. .. ..$ cn : int 2 .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. ..$ tau : num [1:2] 0.312 0.678 .. .. .. ..$ n : int 43920 .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. ..$ x : num [1:2] 0.312 0.678 .. .. .. .. ..$ density: num [1:2] 0.465 0.496 .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" ..$ preserveScale: logi FALSE ..$ scaleFactor : num NA Normalizing betaT using betaN (TumorBoost)...done Setup up data... 'data.frame': 44010 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1145994 2941694 3710825 4240737 4276892 ... $ CT : num 1.63 1.4 1.41 1.17 1.16 ... $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... ..- attr(*, "modelFit")=List of 5 .. ..$ method : chr "normalizeTumorBoost" .. ..$ flavor : chr "v4" .. ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. .. ..- attr(*, "modelFit")=List of 1 .. .. .. ..$ :List of 7 .. .. .. .. ..$ flavor : chr "density" .. .. .. .. ..$ cn : int 2 .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. .. ..$ tau : num [1:2] 0.312 0.678 .. .. .. .. ..$ n : int 43920 .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. .. .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. .. ..$ x : num [1:2] 0.312 0.678 .. .. .. .. .. ..$ density: num [1:2] 0.465 0.496 .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" .. ..$ preserveScale: logi FALSE .. ..$ scaleFactor : num NA $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... ..- attr(*, "modelFit")=List of 1 .. ..$ :List of 7 .. .. ..$ flavor : chr "density" .. .. ..$ cn : int 2 .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. ..$ tau : num [1:2] 0.312 0.678 .. .. ..$ n : int 43920 .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 .. .. .. ..$ density: num [1:5] 1.622 0.465 1.125 0.496 1.587 .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. ..$ x : num [1:2] 0.312 0.678 .. .. .. ..$ density: num [1:2] 0.465 0.496 .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" Setup up data...done Dropping loci for which TCNs are missing... Number of loci dropped: 36 Dropping loci for which TCNs are missing...done Ordering data along genome... 'data.frame': 43974 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Segmenting multiple chromosomes... Number of chromosomes: 3 Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") Produced 3 seeds from this stream for future usage Chromosome #1 ('Chr01') of 3... 'data.frame': 14658 obs. of 8 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... Known segments: [1] chromosome start end <0 rows> (or 0-length row.names) Chromosome #1 ('Chr01') of 3...done Chromosome #2 ('Chr02') of 3... 'data.frame': 14658 obs. of 8 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 14659 14660 14661 14662 14663 14664 14665 14666 14667 14668 ... Known segments: [1] chromosome start end <0 rows> (or 0-length row.names) Chromosome #2 ('Chr02') of 3...done Chromosome #3 ('Chr03') of 3... 'data.frame': 14658 obs. of 8 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 29317 29318 29319 29320 29321 29322 29323 29324 29325 29326 ... Known segments: [1] chromosome start end <0 rows> (or 0-length row.names) Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 3 obs. of 6 variables: ..$ sampleName: chr [1:3] NA NA NA ..$ chromosome: int [1:3] 1 1 1 ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:3] 7599 2668 4391 ..$ mean : num [1:3] 1.39 2.07 2.63 $ segRows:'data.frame': 3 obs. of 2 variables: ..$ startRow: int [1:3] 1 7600 10268 ..$ endRow : int [1:3] 7599 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num -Inf .. ..$ end : num Inf ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.61 0 0.61 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 1 554484 143926517 7599 1.3859 2 1 143926517 185449813 2668 2.0704 3 1 185449813 247137334 4391 2.6341 Number of TCN segments: 3 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.43927e+08]) of 3... Number of TCN loci in segment: 7599 Locus data for TCN segment: 'data.frame': 7599 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7599 Number of SNPs: 2120 (27.90%) Number of heterozygous SNPs: 2120 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7599 obs. of 4 variables: ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7599] NA NA NA NA NA ... ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 554484 ..$ end : num 1.44e+08 ..$ nbrOfLoci : int 2120 ..$ mean : num 0.51 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7594 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 554484 .. ..$ end : num 1.44e+08 ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.07 0 0.06 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7594 int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7594 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 143926517 2120 0.5101 startRow endRow 1 10 7594 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 startRow endRow 1 10 7594 NULL TCN segmentation (expanded) rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 startRow endRow 1 1 7599 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 1 554484 143926517 7599 1.3859 2120 2120 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... Number of TCN loci in segment: 2668 Locus data for TCN segment: 'data.frame': 2668 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... $ CT : num 2.1 2.1 2.09 1.8 2.34 ... $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... $ muN : num 0 1 1 0 0 1 0 0 0 0 ... $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... $ rho : num NA NA NA NA NA NA NA NA NA NA ... Number of loci: 2668 Number of SNPs: 775 (29.05%) Number of heterozygous SNPs: 775 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 3 obs. of 6 variables: ..$ sampleName: chr [1:3] NA NA NA ..$ chromosome: int [1:3] 2 2 2 ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:3] 7599 2668 4391 ..$ mean : num [1:3] 1.39 2.07 2.63 $ segRows:'data.frame': 3 obs. of 2 variables: ..$ startRow: int [1:3] 1 7600 10268 ..$ endRow : int [1:3] 7599 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num -Inf .. ..$ end : num Inf ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.58 0 0.58 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 2 554484 143926517 7599 1.3859 2 2 143926517 185449813 2668 2.0704 3 2 185449813 247137334 4391 2.6341 Number of TCN segments: 3 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.43927e+08]) of 3... Number of TCN loci in segment: 7599 Locus data for TCN segment: Segmenting by CBS...done 'data.frame': 7599 obs. of 9 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7599 Number of SNPs: 2120 (27.90%) Number of heterozygous SNPs: 2120 (100.00%) Chromosome: 2 Segmenting DH signals... Segmenting by CBS... Chromosome: 2 List of 4 $ data :'data.frame': 2668 obs. of 4 variables: ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.44e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 775 ..$ mean : num 0.097 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 15 ..$ endRow : int 2664 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.44e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 DH segmentation (locally-indexed) rows: startRow endRow 1 15 2664 int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... DH segmentation rows: startRow endRow 1 7614 10263 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 143926517 185449813 775 0.097 startRow endRow 1 7614 10263 Rows: [1] 2 TCN segmentation rows: startRow endRow 2 7600 10267 TCN and DH segmentation rows: startRow endRow 2 7600 10267 startRow endRow 1 7614 10263 startRow endRow 1 1 7599 Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 startRow endRow 1 1 7599 2 7600 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 1 143926517 185449813 2668 2.0704 775 775 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 1 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 775 143926517 185449813 775 0.097 Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1314 (29.92%) Number of heterozygous SNPs: 1314 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7599 obs. of 4 variables: ..$ chromosome: int [1:7599] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7599] NA NA NA NA NA ... ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 2 ..$ start : num 554484 ..$ end : num 1.44e+08 ..$ nbrOfLoci : int 2120 ..$ mean : num 0.51 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7594 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num 554484 .. ..$ end : num 1.44e+08 ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.05 0 0.05 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7594 int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7594 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 143926517 2120 0.5101 startRow endRow 1 10 7594 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 startRow endRow 1 10 7594 NULL Segmenting by CBS...done TCN segmentation (expanded) rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 startRow endRow 1 1 7599 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 2 554484 143926517 7599 1.3859 2120 2120 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 2 554484 143926517 7599 1.3859 2120 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... Number of TCN loci in segment: 2668 Locus data for TCN segment: 'data.frame': 2668 obs. of 9 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... $ CT : num 2.1 2.1 2.09 1.8 2.34 ... $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... $ muN : num 0 1 1 0 0 1 0 0 0 0 ... $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... $ rho : num NA NA NA NA NA NA NA NA NA NA ... List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1314 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.04 0 0.03 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 Number of loci: 2668 DH segmentation (locally-indexed) rows: Number of SNPs: 775 (29.05%) Number of heterozygous SNPs: 775 (100.00%) Chromosome: 2 startRow endRow 1 2 4388 Segmenting DH signals... int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done DH segmentation table: Segmenting by CBS... dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1314 0.2295 startRow endRow 1 10269 14655 Rows: [1] 3 TCN segmentation rows: Chromosome: 2 startRow endRow 3 10268 14658 TCN and DH segmentation rows: startRow endRow 3 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7599 2 7600 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 3 10269 14655 startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 1 185449813 247137334 4391 2.6341 1314 1314 (TCN,DH) segmentation for one total CN segment: Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 1314 185449813 247137334 1314 0.2295 Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 2 775 143926517 185449813 775 0.0970 3 1314 185449813 247137334 1314 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 3 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 3 Number of chromosomes: 1 [1] 1 Chromosome 1 ('chr01') of 1... Rows: [1] 1 2 3 Number of segments: 3 TCN segment #1 ('1') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 3...done TCN segment #2 ('2') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 3...done TCN segment #3 ('3') of 3... Nothing todo. Only one DH segmentation. Skipping. Segmenting by CBS...done TCN segment #3 ('3') of 3...done Chromosome 1 ('chr01') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 List of 4 $ data :'data.frame': 2668 obs. of 4 variables: ..$ chromosome: int [1:2668] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 2 ..$ start : num 1.44e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 775 ..$ mean : num 0.097 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 15 ..$ endRow : int 2664 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num 1.44e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.02 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 DH segmentation (locally-indexed) rows: startRow endRow 1 15 2664 int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... DH segmentation rows: startRow endRow 1 7614 10263 Segmenting DH signals...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 143926517 185449813 775 0.097 startRow endRow 1 7614 10263 Rows: [1] 2 TCN segmentation rows: chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 startRow endRow 2 7600 10267 TCN and DH segmentation rows: startRow endRow 2 7600 10267 startRow endRow 1 7614 10263 startRow endRow 1 1 7599 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 startRow endRow 1 1 7599 2 7600 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 2 143926517 185449813 2668 2.0704 775 775 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 2 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 775 143926517 185449813 775 0.097 Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1314 (29.92%) Number of heterozygous SNPs: 1314 (100.00%) Chromosome: 2 Segmenting DH signals... Segmenting by CBS... Chromosome: 2 Chromosome #3 ('Chr03') of 3...done Merging (independently) segmented chromosome... Segmenting paired tumor-normal signals using Paired PSCBS... Setup up data... Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Setup up data...done Ordering data along genome... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Keeping only current chromosome for 'knownSegments'... Chromosome: 3 Known segments for this chromosome: [1] chromosome start end <0 rows> (or 0-length row.names) Keeping only current chromosome for 'knownSegments'...done alphaTCN: 0.009 alphaDH: 0.001 Number of loci: 14658 Calculating DHs... Number of SNPs: 14658 Number of heterozygous SNPs: 4209 (28.71%) Normalized DHs: num [1:14658] NA NA NA NA NA ... Calculating DHs...done Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") Produced 2 seeds from this stream for future usage Identification of change points by total copy numbers... Segmenting by CBS... Chromosome: 3 Segmenting by CBS...done List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 2 2 2 2 2 2 2 2 2 2 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 2 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1314 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 2 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.03 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 DH segmentation (locally-indexed) rows: startRow endRow 1 2 4388 int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1314 0.2295 startRow endRow 1 10269 14655 Rows: [1] 3 TCN segmentation rows: startRow endRow 3 10268 14658 TCN and DH segmentation rows: startRow endRow 3 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7599 2 7600 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 3 10269 14655 startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 2 185449813 247137334 4391 2.6341 1314 1314 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 2 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 1314 185449813 247137334 1314 0.2295 Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 2 775 143926517 185449813 775 0.0970 3 1314 185449813 247137334 1314 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 3 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 3 Number of chromosomes: 1 [1] 2 Chromosome 1 ('chr02') of 1... Rows: [1] 1 2 3 Number of segments: 3 TCN segment #1 ('1') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 3...done TCN segment #2 ('2') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 3...done TCN segment #3 ('3') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #3 ('3') of 3...done Chromosome 1 ('chr02') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 2 1 1 554484 143926517 7599 1.3859 2120 2 2 2 1 143926517 185449813 2668 2.0704 775 3 2 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 3 obs. of 6 variables: ..$ sampleName: chr [1:3] NA NA NA ..$ chromosome: int [1:3] 3 3 3 ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:3] 7599 2668 4391 ..$ mean : num [1:3] 1.39 2.07 2.63 $ segRows:'data.frame': 3 obs. of 2 variables: ..$ startRow: int [1:3] 1 7600 10268 ..$ endRow : int [1:3] 7599 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num -Inf .. ..$ end : num Inf ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.58 0 0.58 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 3 554484 143926517 7599 1.3859 2 3 143926517 185449813 2668 2.0704 3 3 185449813 247137334 4391 2.6341 Number of TCN segments: 3 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.43927e+08]) of 3... Number of TCN loci in segment: 7599 Locus data for TCN segment: 'data.frame': 7599 obs. of 9 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7599 Number of SNPs: 2120 (27.90%) Number of heterozygous SNPs: 2120 (100.00%) Chromosome: 3 Segmenting DH signals... Segmenting by CBS... Chromosome: 3 Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7599 obs. of 4 variables: ..$ chromosome: int [1:7599] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7599] NA NA NA NA NA ... ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 3 ..$ start : num 554484 ..$ end : num 1.44e+08 ..$ nbrOfLoci : int 2120 ..$ mean : num 0.51 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7594 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num 554484 .. ..$ end : num 1.44e+08 ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.06 0 0.06 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7594 int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7594 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 143926517 2120 0.5101 startRow endRow 1 10 7594 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 startRow endRow 1 10 7594 NULL TCN segmentation (expanded) rows: startRow endRow 1 1 7599 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 startRow endRow 1 1 7599 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 3 554484 143926517 7599 1.3859 2120 2120 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 3 554484 143926517 7599 1.3859 2120 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... Number of TCN loci in segment: 2668 Locus data for TCN segment: 'data.frame': 2668 obs. of 9 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... $ CT : num 2.1 2.1 2.09 1.8 2.34 ... $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... $ muN : num 0 1 1 0 0 1 0 0 0 0 ... $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... $ rho : num NA NA NA NA NA NA NA NA NA NA ... Number of loci: 2668 Number of SNPs: 775 (29.05%) Number of heterozygous SNPs: 775 (100.00%) Chromosome: 3 Segmenting DH signals... Segmenting by CBS... Chromosome: 3 Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 2668 obs. of 4 variables: ..$ chromosome: int [1:2668] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 3 ..$ start : num 1.44e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 775 ..$ mean : num 0.097 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 15 ..$ endRow : int 2664 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num 1.44e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.02 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 DH segmentation (locally-indexed) rows: startRow endRow 1 15 2664 int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... DH segmentation rows: startRow endRow 1 7614 10263 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 143926517 185449813 775 0.097 startRow endRow 1 7614 10263 Rows: [1] 2 TCN segmentation rows: startRow endRow 2 7600 10267 TCN and DH segmentation rows: startRow endRow 2 7600 10267 startRow endRow 1 7614 10263 startRow endRow 1 1 7599 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 startRow endRow 1 1 7599 2 7600 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 3 143926517 185449813 2668 2.0704 775 775 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 3 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 775 143926517 185449813 775 0.097 Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1314 (29.92%) Number of heterozygous SNPs: 1314 (100.00%) Chromosome: 3 Segmenting DH signals... Segmenting by CBS... Chromosome: 3 Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 3 3 3 3 3 3 3 3 3 3 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 3 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1314 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 3 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.04 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 DH segmentation (locally-indexed) rows: startRow endRow 1 2 4388 int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1314 0.2295 startRow endRow 1 10269 14655 Rows: [1] 3 TCN segmentation rows: startRow endRow 3 10268 14658 TCN and DH segmentation rows: startRow endRow 3 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7599 2 7600 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 startRow endRow 1 10 7594 2 7614 10263 3 10269 14655 startRow endRow 1 1 7599 2 7600 10267 3 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 3 185449813 247137334 4391 2.6341 1314 1314 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 3 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 1314 185449813 247137334 1314 0.2295 Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2120 554484 143926517 2120 0.5101 2 775 143926517 185449813 775 0.0970 3 1314 185449813 247137334 1314 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 3 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 3 Number of chromosomes: 1 [1] 3 Chromosome 1 ('chr03') of 1... Rows: [1] 1 2 3 Number of segments: 3 TCN segment #1 ('1') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 3...done TCN segment #2 ('2') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 3...done TCN segment #3 ('3') of 3... Nothing todo. Only one DH segmentation. Skipping. TCN segment #3 ('3') of 3...done Chromosome 1 ('chr03') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 3 1 1 554484 143926517 7599 1.3859 2120 2 3 2 1 143926517 185449813 2668 2.0704 775 3 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 List of 5 $ data :Classes 'PairedPSCNData' and 'data.frame': 43974 obs. of 8 variables: ..$ chromosome: int [1:43974] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:43974] 554484 730720 782343 878522 916294 ... ..$ CT : num [1:43974] 1.88 1.8 1.59 1.64 1.53 ... ..$ betaT : num [1:43974] 0.0646 0.1672 0.9284 0.113 0.7209 ... ..$ betaTN : num [1:43974] -0.0515 -0.1172 1.0194 0.031 0.8604 ... ..$ betaN : num [1:43974] 0.116 0.284 0.909 0.082 0.86 ... ..$ muN : num [1:43974] 0 0 1 0 1 1 1 0 1 0.5 ... ..$ rho : num [1:43974] NA NA NA NA NA ... $ output :Classes 'PairedPSCNSegments' and 'data.frame': 11 obs. of 15 variables: ..$ chromosome : int [1:11] 1 1 1 NA 2 2 2 NA 3 3 ... ..$ tcnId : int [1:11] 1 2 3 NA 1 2 3 NA 1 2 ... ..$ dhId : int [1:11] 1 1 1 NA 1 1 1 NA 1 1 ... ..$ tcnStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... ..$ tcnEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... ..$ tcnNbrOfLoci: int [1:11] 7599 2668 4391 NA 7599 2668 4391 NA 7599 2668 ... ..$ tcnMean : num [1:11] 1.39 2.07 2.63 NA 1.39 ... ..$ tcnNbrOfSNPs: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... ..$ tcnNbrOfHets: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... ..$ dhStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... ..$ dhEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... ..$ dhNbrOfLoci : int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... ..$ dhMean : num [1:11] 0.51 0.097 0.23 NA 0.51 ... ..$ c1Mean : num [1:11] 0.339 0.935 1.015 NA 0.339 ... ..$ c2Mean : num [1:11] 1.05 1.14 1.62 NA 1.05 ... $ tcnSegRows:'data.frame': 11 obs. of 2 variables: ..$ startRow: int [1:11] 1 7600 10268 NA 14659 22258 24926 NA 29317 36916 ... ..$ endRow : int [1:11] 7599 10267 14658 NA 22257 24925 29316 NA 36915 39583 ... $ dhSegRows :'data.frame': 11 obs. of 2 variables: ..$ startRow: int [1:11] 10 7614 10269 NA 14668 22272 24927 NA 29326 36930 ... ..$ endRow : int [1:11] 7594 10263 14655 NA 22252 24921 29313 NA 36910 39579 ... $ params :List of 7 ..$ alphaTCN : num 0.009 ..$ alphaDH : num 0.001 ..$ flavor : chr "tcn&dh" ..$ tbn : logi FALSE ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 0 obs. of 3 variables: .. ..$ chromosome: int(0) .. ..$ start : int(0) .. ..$ end : int(0) ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" Merging (independently) segmented chromosome...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 143926517 7599 1.3859 2120 2 1 2 1 143926517 185449813 2668 2.0704 775 3 1 3 1 185449813 247137334 4391 2.6341 1314 4 NA NA NA NA NA NA NA NA 5 2 1 1 554484 143926517 7599 1.3859 2120 6 2 2 1 143926517 185449813 2668 2.0704 775 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 4 NA NA NA NA NA NA NA 5 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 6 2 2 1 143926517 185449813 2668 2.0704 775 7 2 3 1 185449813 247137334 4391 2.6341 1314 8 NA NA NA NA NA NA NA NA 9 3 1 1 554484 143926517 7599 1.3859 2120 10 3 2 1 143926517 185449813 2668 2.0704 775 11 3 3 1 185449813 247137334 4391 2.6341 1314 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 7 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 8 NA NA NA NA NA NA NA 9 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 10 775 143926517 185449813 775 0.0970 0.9347856 1.135614 11 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 Segmenting multiple chromosomes...done Segmenting paired tumor-normal signals using Paired PSCBS...done > > message("*** segmentByPairedPSCBS() via futures ... DONE") *** segmentByPairedPSCBS() via futures ... DONE > > > message("*** segmentByPairedPSCBS() via futures with known segments ...") *** segmentByPairedPSCBS() via futures with known segments ... > fits <- list() > dataT <- subset(data, chromosome == 1) > gaps <- findLargeGaps(dataT, minLength=2e6) > knownSegments <- gapsToSegments(gaps) > > for (strategy in strategies) { + message(sprintf("- segmentByPairedPSCBS() w/ known segments using '%s' futures ...", strategy)) + plan(strategy) + fit <- segmentByPairedPSCBS(dataT, knownSegments=knownSegments, seed=0xBEEF, verbose=TRUE) + fits[[strategy]] <- fit + equal <- all.equal(fit, fits[[1]]) + if (!equal) { + str(fit) + str(fits[[1]]) + print(equal) + stop(sprintf("segmentByPairedPSCBS() w/ known segments using '%s' futures does not produce the same results as when using '%s' futures", strategy, names(fits)[1])) + } + } - segmentByPairedPSCBS() w/ known segments using 'sequential' futures ... Segmenting paired tumor-normal signals using Paired PSCBS... Calling genotypes from normal allele B fractions... num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... Called genotypes: num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... - attr(*, "modelFit")=List of 1 ..$ :List of 7 .. ..$ flavor : chr "density" .. ..$ cn : int 2 .. ..$ nbrOfGenotypeGroups: int 3 .. ..$ tau : num [1:2] 0.315 0.677 .. ..$ n : int 14640 .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. ..$ type : chr [1:2] "valley" "valley" .. .. ..$ x : num [1:2] 0.315 0.677 .. .. ..$ density: num [1:2] 0.522 0.551 ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" muN 0 0.5 1 5221 4198 5251 Calling genotypes from normal allele B fractions...done Normalizing betaT using betaN (TumorBoost)... Normalized BAFs: num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... - attr(*, "modelFit")=List of 5 ..$ method : chr "normalizeTumorBoost" ..$ flavor : chr "v4" ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. ..- attr(*, "modelFit")=List of 1 .. .. ..$ :List of 7 .. .. .. ..$ flavor : chr "density" .. .. .. ..$ cn : int 2 .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. ..$ tau : num [1:2] 0.315 0.677 .. .. .. ..$ n : int 14640 .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. ..$ x : num [1:2] 0.315 0.677 .. .. .. .. ..$ density: num [1:2] 0.522 0.551 .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" ..$ preserveScale: logi FALSE ..$ scaleFactor : num NA Normalizing betaT using betaN (TumorBoost)...done Setup up data... 'data.frame': 14670 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1145994 2941694 3710825 4240737 4276892 ... $ CT : num 1.63 1.4 1.41 1.17 1.16 ... $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... ..- attr(*, "modelFit")=List of 5 .. ..$ method : chr "normalizeTumorBoost" .. ..$ flavor : chr "v4" .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. .. ..- attr(*, "modelFit")=List of 1 .. .. .. ..$ :List of 7 .. .. .. .. ..$ flavor : chr "density" .. .. .. .. ..$ cn : int 2 .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 .. .. .. .. ..$ n : int 14640 .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. .. .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 .. .. .. .. .. ..$ density: num [1:2] 0.522 0.551 .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" .. ..$ preserveScale: logi FALSE .. ..$ scaleFactor : num NA $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... ..- attr(*, "modelFit")=List of 1 .. ..$ :List of 7 .. .. ..$ flavor : chr "density" .. .. ..$ cn : int 2 .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. ..$ tau : num [1:2] 0.315 0.677 .. .. ..$ n : int 14640 .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. ..$ x : num [1:2] 0.315 0.677 .. .. .. ..$ density: num [1:2] 0.522 0.551 .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" Setup up data...done Dropping loci for which TCNs are missing... Number of loci dropped: 12 Dropping loci for which TCNs are missing...done Ordering data along genome... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Keeping only current chromosome for 'knownSegments'... Chromosome: 1 Known segments for this chromosome: chromosome start end length 1 1 -Inf 120908858 Inf 2 1 120908859 142693887 21785028 3 1 142693888 Inf Inf Keeping only current chromosome for 'knownSegments'...done alphaTCN: 0.009 alphaDH: 0.001 Number of loci: 14658 Calculating DHs... Number of SNPs: 14658 Number of heterozygous SNPs: 4196 (28.63%) Normalized DHs: num [1:14658] NA NA NA NA NA ... Calculating DHs...done Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") Produced 2 seeds from this stream for future usage Identification of change points by total copy numbers... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") Produced 3 seeds from this stream for future usage Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 4 obs. of 6 variables: ..$ sampleName: chr [1:4] NA NA NA NA ..$ chromosome: int [1:4] 1 1 1 1 ..$ start : num [1:4] 5.54e+05 1.21e+08 1.43e+08 1.85e+08 ..$ end : num [1:4] 1.21e+08 1.43e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 ..$ mean : num [1:4] 1.39 NA 2.07 2.63 $ segRows:'data.frame': 4 obs. of 2 variables: ..$ startRow: int [1:4] 1 NA 7587 10268 ..$ endRow : int [1:4] 7586 NA 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 4 obs. of 3 variables: .. ..$ chromosome: int [1:4] 1 1 2 1 .. ..$ start : num [1:4] -Inf -Inf -Inf 1.43e+08 .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.21 0 0.22 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 1 554484 120908858 7586 1.3853 2 1 120908859 142693887 0 NA 3 1 142693888 185449813 2681 2.0689 4 1 185449813 247137334 4391 2.6341 Number of TCN segments: 4 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.20909e+08]) of 4... Number of TCN loci in segment: 7586 Locus data for TCN segment: 'data.frame': 7586 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7586 Number of SNPs: 2108 (27.79%) Number of heterozygous SNPs: 2108 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7586 obs. of 4 variables: ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7586] NA NA NA NA NA ... ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 554484 ..$ end : num 1.21e+08 ..$ nbrOfLoci : int 2108 ..$ mean : num 0.512 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7574 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 554484 .. ..$ end : num 1.21e+08 ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.09 0 0.09 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7574 int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7574 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 120908858 2108 0.5116 startRow endRow 1 10 7574 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7586 TCN and DH segmentation rows: startRow endRow 1 1 7586 startRow endRow 1 10 7574 NULL TCN segmentation (expanded) rows: startRow endRow 1 1 7586 TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 startRow endRow 1 1 7586 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 1 554484 120908858 7586 1.3853 2108 2108 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2108 554484 120908858 2108 0.5116 Total CN segment #1 ([ 554484,1.20909e+08]) of 4...done Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4... Number of TCN loci in segment: 0 Locus data for TCN segment: 'data.frame': 0 obs. of 9 variables: $ chromosome: int $ x : num $ CT : num $ betaT : num $ betaTN : num $ betaN : num $ muN : num $ index : int $ rho : num Number of loci: 0 Number of SNPs: 0 (NaN%) Number of heterozygous SNPs: 0 (NaN%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: NA Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 0 obs. of 4 variables: ..$ chromosome: int(0) ..$ x : num(0) ..$ y : num(0) ..$ index : int(0) $ output :'data.frame': 0 obs. of 6 variables: ..$ sampleName: chr(0) ..$ chromosome: num(0) ..$ start : num(0) ..$ end : num(0) ..$ nbrOfLoci : int(0) ..$ mean : num(0) $ segRows:'data.frame': 0 obs. of 2 variables: ..$ startRow: int(0) ..$ endRow : int(0) $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 0 obs. of 3 variables: .. ..$ chromosome: int(0) .. ..$ start : num(0) .. ..$ end : num(0) ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0 0 0 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: [1] startRow endRow <0 rows> (or 0-length row.names) int(0) DH segmentation rows: [1] startRow endRow <0 rows> (or 0-length row.names) Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean NA NA NA NA NA startRow endRow NA NA NA Rows: [1] 2 TCN segmentation rows: startRow endRow 2 NA NA TCN and DH segmentation rows: startRow endRow 2 NA NA startRow endRow NA NA NA startRow endRow 1 1 7586 TCN segmentation (expanded) rows: startRow endRow 1 1 7586 2 NA NA TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 2 NA NA startRow endRow 1 1 7586 2 NA NA Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 1 120908859 142693887 0 NA 0 0 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 1 120908859 142693887 0 NA 0 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 0 NA NA NA NA Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4...done Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4... Number of TCN loci in segment: 2681 Locus data for TCN segment: 'data.frame': 2681 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... $ CT : num 2.27 1.55 1.47 1.5 1.81 ... $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... $ rho : num 0.117 0.258 NA NA NA ... Number of loci: 2681 Number of SNPs: 777 (28.98%) Number of heterozygous SNPs: 777 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 2681 obs. of 4 variables: ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.43e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 777 ..$ mean : num 0.0973 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 1 ..$ endRow : int 2677 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.43e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0 0 0 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: startRow endRow 1 1 2677 int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... DH segmentation rows: startRow endRow 1 7587 10263 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 142693888 185449813 777 0.0973 startRow endRow 1 7587 10263 Rows: [1] 3 TCN segmentation rows: startRow endRow 3 7587 10267 TCN and DH segmentation rows: startRow endRow 3 7587 10267 startRow endRow 1 7587 10263 startRow endRow 1 1 7586 2 NA NA TCN segmentation (expanded) rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 2 NA NA 3 7587 10263 startRow endRow 1 1 7586 2 NA NA 3 7587 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 1 142693888 185449813 2681 2.0689 777 777 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 1 142693888 185449813 2681 2.0689 777 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 777 142693888 185449813 777 0.0973 Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4...done Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1311 (29.86%) Number of heterozygous SNPs: 1311 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1311 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: startRow endRow 1 2 4388 int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1311 0.2295 startRow endRow 1 10269 14655 Rows: [1] 4 TCN segmentation rows: startRow endRow 4 10268 14658 TCN and DH segmentation rows: startRow endRow 4 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7586 2 NA NA 3 7587 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 2 NA NA 3 7587 10263 4 10269 14655 startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 4 1 185449813 247137334 4391 2.6341 1311 1311 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 4 4 1 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 4 1311 185449813 247137334 1311 0.2295 Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 2 1 2 1 120908859 142693887 0 NA 0 3 1 3 1 142693888 185449813 2681 2.0689 777 4 1 4 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2108 554484 120908858 2108 0.5116 2 0 NA NA NA NA 3 777 142693888 185449813 777 0.0973 4 1311 185449813 247137334 1311 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 4 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 4 Number of chromosomes: 1 [1] 1 Chromosome 1 ('chr01') of 1... Rows: [1] 1 2 3 4 Number of segments: 4 TCN segment #1 ('1') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 4...done TCN segment #2 ('2') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 4...done TCN segment #3 ('3') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #3 ('3') of 4...done TCN segment #4 ('4') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #4 ('4') of 4...done Chromosome 1 ('chr01') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 2 1 2 1 120908859 142693887 0 NA 0 3 1 3 1 142693888 185449813 2681 2.0689 777 4 1 4 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 2 0 NA NA NA NA NA NA 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 2 1 2 1 120908859 142693887 0 NA 0 3 1 3 1 142693888 185449813 2681 2.0689 777 4 1 4 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 2 0 NA NA NA NA NA NA 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 - segmentByPairedPSCBS() w/ known segments using 'multisession' futures ... Segmenting paired tumor-normal signals using Paired PSCBS... Calling genotypes from normal allele B fractions... num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... Called genotypes: num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... - attr(*, "modelFit")=List of 1 ..$ :List of 7 .. ..$ flavor : chr "density" .. ..$ cn : int 2 .. ..$ nbrOfGenotypeGroups: int 3 .. ..$ tau : num [1:2] 0.315 0.677 .. ..$ n : int 14640 .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. ..$ type : chr [1:2] "valley" "valley" .. .. ..$ x : num [1:2] 0.315 0.677 .. .. ..$ density: num [1:2] 0.522 0.551 ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" muN 0 0.5 1 5221 4198 5251 Calling genotypes from normal allele B fractions...done Normalizing betaT using betaN (TumorBoost)... Normalized BAFs: num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... - attr(*, "modelFit")=List of 5 ..$ method : chr "normalizeTumorBoost" ..$ flavor : chr "v4" ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. ..- attr(*, "modelFit")=List of 1 .. .. ..$ :List of 7 .. .. .. ..$ flavor : chr "density" .. .. .. ..$ cn : int 2 .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. ..$ tau : num [1:2] 0.315 0.677 .. .. .. ..$ n : int 14640 .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. ..$ x : num [1:2] 0.315 0.677 .. .. .. .. ..$ density: num [1:2] 0.522 0.551 .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" ..$ preserveScale: logi FALSE ..$ scaleFactor : num NA Normalizing betaT using betaN (TumorBoost)...done Setup up data... 'data.frame': 14670 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1145994 2941694 3710825 4240737 4276892 ... $ CT : num 1.63 1.4 1.41 1.17 1.16 ... $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... ..- attr(*, "modelFit")=List of 5 .. ..$ method : chr "normalizeTumorBoost" .. ..$ flavor : chr "v4" .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... .. .. ..- attr(*, "modelFit")=List of 1 .. .. .. ..$ :List of 7 .. .. .. .. ..$ flavor : chr "density" .. .. .. .. ..$ cn : int 2 .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 .. .. .. .. ..$ n : int 14640 .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. .. .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 .. .. .. .. .. ..$ density: num [1:2] 0.522 0.551 .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" .. ..$ preserveScale: logi FALSE .. ..$ scaleFactor : num NA $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... ..- attr(*, "modelFit")=List of 1 .. ..$ :List of 7 .. .. ..$ flavor : chr "density" .. .. ..$ cn : int 2 .. .. ..$ nbrOfGenotypeGroups: int 3 .. .. ..$ tau : num [1:2] 0.315 0.677 .. .. ..$ n : int 14640 .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 .. .. .. ..$ density: num [1:5] 1.479 0.522 1.056 0.551 1.453 .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: .. .. .. ..$ type : chr [1:2] "valley" "valley" .. .. .. ..$ x : num [1:2] 0.315 0.677 .. .. .. ..$ density: num [1:2] 0.522 0.551 .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" Setup up data...done Dropping loci for which TCNs are missing... Number of loci dropped: 12 Dropping loci for which TCNs are missing...done Ordering data along genome... 'data.frame': 14658 obs. of 7 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... Ordering data along genome...done Keeping only current chromosome for 'knownSegments'... Chromosome: 1 Known segments for this chromosome: chromosome start end length 1 1 -Inf 120908858 Inf 2 1 120908859 142693887 21785028 3 1 142693888 Inf Inf Keeping only current chromosome for 'knownSegments'...done alphaTCN: 0.009 alphaDH: 0.001 Number of loci: 14658 Calculating DHs... Number of SNPs: 14658 Number of heterozygous SNPs: 4196 (28.63%) Normalized DHs: num [1:14658] NA NA NA NA NA ... Calculating DHs...done Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") Produced 2 seeds from this stream for future usage Identification of change points by total copy numbers... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") Produced 3 seeds from this stream for future usage Segmenting by CBS...done List of 4 $ data :'data.frame': 14658 obs. of 4 variables: ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 4 obs. of 6 variables: ..$ sampleName: chr [1:4] NA NA NA NA ..$ chromosome: int [1:4] 1 1 1 1 ..$ start : num [1:4] 5.54e+05 1.21e+08 1.43e+08 1.85e+08 ..$ end : num [1:4] 1.21e+08 1.43e+08 1.85e+08 2.47e+08 ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 ..$ mean : num [1:4] 1.39 NA 2.07 2.63 $ segRows:'data.frame': 4 obs. of 2 variables: ..$ startRow: int [1:4] 1 NA 7587 10268 ..$ endRow : int [1:4] 7586 NA 10267 14658 $ params :List of 5 ..$ alpha : num 0.009 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 4 obs. of 3 variables: .. ..$ chromosome: int [1:4] 1 1 2 1 .. ..$ start : num [1:4] -Inf -Inf -Inf 1.43e+08 .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.24 0 0.24 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 Identification of change points by total copy numbers...done Restructure TCN segmentation results... chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 1 1 554484 120908858 7586 1.3853 2 1 120908859 142693887 0 NA 3 1 142693888 185449813 2681 2.0689 4 1 185449813 247137334 4391 2.6341 Number of TCN segments: 4 Restructure TCN segmentation results...done Total CN segment #1 ([ 554484,1.20909e+08]) of 4... Number of TCN loci in segment: 7586 Locus data for TCN segment: 'data.frame': 7586 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 554484 730720 782343 878522 916294 ... $ CT : num 1.88 1.8 1.59 1.64 1.53 ... $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... $ index : int 1 2 3 4 5 6 7 8 9 10 ... $ rho : num NA NA NA NA NA ... Number of loci: 7586 Number of SNPs: 2108 (27.79%) Number of heterozygous SNPs: 2108 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 7586 obs. of 4 variables: ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... ..$ y : num [1:7586] NA NA NA NA NA ... ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 554484 ..$ end : num 1.21e+08 ..$ nbrOfLoci : int 2108 ..$ mean : num 0.512 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 10 ..$ endRow : int 7574 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 554484 .. ..$ end : num 1.21e+08 ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.08 0 0.08 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: startRow endRow 1 10 7574 int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... DH segmentation rows: startRow endRow 1 10 7574 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 554484 120908858 2108 0.5116 startRow endRow 1 10 7574 Rows: [1] 1 TCN segmentation rows: startRow endRow 1 1 7586 TCN and DH segmentation rows: startRow endRow 1 1 7586 startRow endRow 1 10 7574 NULL TCN segmentation (expanded) rows: startRow endRow 1 1 7586 TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 startRow endRow 1 1 7586 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 1 1 554484 120908858 7586 1.3853 2108 2108 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2108 554484 120908858 2108 0.5116 Total CN segment #1 ([ 554484,1.20909e+08]) of 4...done Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4... Number of TCN loci in segment: 0 Locus data for TCN segment: 'data.frame': 0 obs. of 9 variables: $ chromosome: int $ x : num $ CT : num $ betaT : num $ betaTN : num $ betaN : num $ muN : num $ index : int $ rho : num Number of loci: 0 Number of SNPs: 0 (NaN%) Number of heterozygous SNPs: 0 (NaN%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: NA Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 0 obs. of 4 variables: ..$ chromosome: int(0) ..$ x : num(0) ..$ y : num(0) ..$ index : int(0) $ output :'data.frame': 0 obs. of 6 variables: ..$ sampleName: chr(0) ..$ chromosome: num(0) ..$ start : num(0) ..$ end : num(0) ..$ nbrOfLoci : int(0) ..$ mean : num(0) $ segRows:'data.frame': 0 obs. of 2 variables: ..$ startRow: int(0) ..$ endRow : int(0) $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 0 obs. of 3 variables: .. ..$ chromosome: int(0) .. ..$ start : num(0) .. ..$ end : num(0) ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0 0 0 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: [1] startRow endRow <0 rows> (or 0-length row.names) int(0) DH segmentation rows: [1] startRow endRow <0 rows> (or 0-length row.names) Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean NA NA NA NA NA startRow endRow NA NA NA Rows: [1] 2 TCN segmentation rows: startRow endRow 2 NA NA TCN and DH segmentation rows: startRow endRow 2 NA NA startRow endRow NA NA NA startRow endRow 1 1 7586 TCN segmentation (expanded) rows: startRow endRow 1 1 7586 2 NA NA TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 2 NA NA startRow endRow 1 1 7586 2 NA NA Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 2 1 120908859 142693887 0 NA 0 0 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 2 2 1 1 120908859 142693887 0 NA 0 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 2 0 NA NA NA NA Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4...done Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4... Number of TCN loci in segment: 2681 Locus data for TCN segment: 'data.frame': 2681 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... $ CT : num 2.27 1.55 1.47 1.5 1.81 ... $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... $ rho : num 0.117 0.258 NA NA NA ... Number of loci: 2681 Number of SNPs: 777 (28.98%) Number of heterozygous SNPs: 777 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 2681 obs. of 4 variables: ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.43e+08 ..$ end : num 1.85e+08 ..$ nbrOfLoci : int 777 ..$ mean : num 0.0973 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 1 ..$ endRow : int 2677 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.43e+08 .. ..$ end : num 1.85e+08 ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: startRow endRow 1 1 2677 int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... DH segmentation rows: startRow endRow 1 7587 10263 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 142693888 185449813 777 0.0973 startRow endRow 1 7587 10263 Rows: [1] 3 TCN segmentation rows: startRow endRow 3 7587 10267 TCN and DH segmentation rows: startRow endRow 3 7587 10267 startRow endRow 1 7587 10263 startRow endRow 1 1 7586 2 NA NA TCN segmentation (expanded) rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 2 NA NA 3 7587 10263 startRow endRow 1 1 7586 2 NA NA 3 7587 10267 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 3 1 142693888 185449813 2681 2.0689 777 777 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 3 3 1 1 142693888 185449813 2681 2.0689 777 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 3 777 142693888 185449813 777 0.0973 Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4...done Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... Number of TCN loci in segment: 4391 Locus data for TCN segment: 'data.frame': 4391 obs. of 9 variables: $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... $ CT : num 2.93 2.15 2.82 2.93 2.46 ... $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... $ rho : num NA 0.2186 NA 0.0503 NA ... Number of loci: 4391 Number of SNPs: 1311 (29.86%) Number of heterozygous SNPs: 1311 (100.00%) Chromosome: 1 Segmenting DH signals... Segmenting by CBS... Chromosome: 1 Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") Segmenting by CBS...done List of 4 $ data :'data.frame': 4391 obs. of 4 variables: ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... $ output :'data.frame': 1 obs. of 6 variables: ..$ sampleName: chr NA ..$ chromosome: int 1 ..$ start : num 1.85e+08 ..$ end : num 2.47e+08 ..$ nbrOfLoci : int 1311 ..$ mean : num 0.23 $ segRows:'data.frame': 1 obs. of 2 variables: ..$ startRow: int 2 ..$ endRow : int 4388 $ params :List of 5 ..$ alpha : num 0.001 ..$ undo : num 0 ..$ joinSegments : logi TRUE ..$ knownSegments:'data.frame': 1 obs. of 3 variables: .. ..$ chromosome: int 1 .. ..$ start : num 1.85e+08 .. ..$ end : num 2.47e+08 ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.03 NA NA ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 DH segmentation (locally-indexed) rows: startRow endRow 1 2 4388 int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... DH segmentation rows: startRow endRow 1 10269 14655 Segmenting DH signals...done DH segmentation table: dhStart dhEnd dhNbrOfLoci dhMean 1 185449813 247137334 1311 0.2295 startRow endRow 1 10269 14655 Rows: [1] 4 TCN segmentation rows: startRow endRow 4 10268 14658 TCN and DH segmentation rows: startRow endRow 4 10268 14658 startRow endRow 1 10269 14655 startRow endRow 1 1 7586 2 NA NA 3 7587 10267 TCN segmentation (expanded) rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 TCN and DH segmentation rows: startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 startRow endRow 1 10 7574 2 NA NA 3 7587 10263 4 10269 14655 startRow endRow 1 1 7586 2 NA NA 3 7587 10267 4 10268 14658 Total CN segmentation table (expanded): chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 4 1 185449813 247137334 4391 2.6341 1311 1311 (TCN,DH) segmentation for one total CN segment: tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 4 4 1 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 4 1311 185449813 247137334 1311 0.2295 Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 2 1 2 1 120908859 142693887 0 NA 0 3 1 3 1 142693888 185449813 2681 2.0689 777 4 1 4 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 1 2108 554484 120908858 2108 0.5116 2 0 NA NA NA NA 3 777 142693888 185449813 777 0.0973 4 1311 185449813 247137334 1311 0.2295 Calculating (C1,C2) per segment... Calculating (C1,C2) per segment...done Number of segments: 4 Segmenting paired tumor-normal signals using Paired PSCBS...done Post-segmenting TCNs... Number of segments: 4 Number of chromosomes: 1 [1] 1 Chromosome 1 ('chr01') of 1... Rows: [1] 1 2 3 4 Number of segments: 4 TCN segment #1 ('1') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #1 ('1') of 4...done TCN segment #2 ('2') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #2 ('2') of 4...done TCN segment #3 ('3') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #3 ('3') of 4...done TCN segment #4 ('4') of 4... Nothing todo. Only one DH segmentation. Skipping. TCN segment #4 ('4') of 4...done Chromosome 1 ('chr01') of 1...done Update (C1,C2) per segment... Update (C1,C2) per segment...done Post-segmenting TCNs...done chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 2 1 2 1 120908859 142693887 0 NA 0 3 1 3 1 142693888 185449813 2681 2.0689 777 4 1 4 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 2 0 NA NA NA NA NA NA 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 1 1 1 1 554484 120908858 7586 1.3853 2108 2 1 2 1 120908859 142693887 0 NA 0 3 1 3 1 142693888 185449813 2681 2.0689 777 4 1 4 1 185449813 247137334 4391 2.6341 1311 tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 2 0 NA NA NA NA NA NA 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 > > message("*** segmentByPairedPSCBS() via futures ... DONE") *** segmentByPairedPSCBS() via futures ... DONE > > > ## Cleanup > plan(oplan) > rm(list=c("fits", "data", "fit")) > > proc.time() user system elapsed 5.84 0.18 11.61