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Type 'q()' to quit R. > library(CloneSeeker) > > dataPars <- list(snps.seq = 1000000, + snps.cgh = 600000, + mu = 70, + sigma.reads = 25, + sigma0.lrr = 0.15, + sigma0.baf = 0.03, + density.sigma = 0.1) > psis <- c(0.6, 0.3, 0.1) > > suppressWarnings( RNGversion("3.5.0") ) > set.seed(412634) > ### Mutations only? without contamination > tumor <- Tumor(psis, rounds = 400, nu = 100, pcnv = 0, norm.contam = FALSE) > clone <- getClone(tumor, 1) > summary(clone$cn) # why is the parent index constant? chr start end A Min. : 1.000 Min. : 1 Min. : 321330 Min. :1 1st Qu.: 4.000 1st Qu.: 41677134 1st Qu.: 62620640 1st Qu.:1 Median : 9.000 Median :121340754 Median :136090569 Median :1 Mean : 9.797 Mean :114810620 Mean :134999686 Mean :1 3rd Qu.:15.000 3rd Qu.:185143852 3rd Qu.:207375478 3rd Qu.:1 Max. :24.000 Max. :248606021 Max. :249250621 Max. :1 B seg parent.index Min. :1 Min. : 1.00 Min. :84 1st Qu.:1 1st Qu.: 74.75 1st Qu.:84 Median :1 Median :148.50 Median :84 Mean :1 Mean :148.50 Mean :84 3rd Qu.:1 3rd Qu.:222.25 3rd Qu.:84 Max. :1 Max. :296.00 Max. :84 > summary(clone$seq) chr start seg mut.id Min. : 1.000 Min. : 1878 Min. : 2 Min. : 51 1st Qu.: 4.000 1st Qu.: 32597133 1st Qu.: 70 1st Qu.: 3327 Median : 8.000 Median : 69992560 Median :136 Median : 4778 Mean : 9.184 Mean : 78684555 Mean :139 Mean : 5535 3rd Qu.:13.000 3rd Qu.:112177800 3rd Qu.:206 3rd Qu.: 8119 Max. :24.000 Max. :246484357 Max. :291 Max. :14115 mutated.copies allele normal.copies Min. :1 A:287 Min. :1 1st Qu.:1 B:267 1st Qu.:1 Median :1 Median :1 Mean :1 Mean :1 3rd Qu.:1 3rd Qu.:1 Max. :1 Max. :1 > > ### Mutations only? with normal contamination > tumor <- Tumor(psis, rounds = 400, nu = 100, pcnv = 0, norm.contam = TRUE) > clone <- getClone(tumor, 1) > summary(clone$cn) # why is the parent index missing? chr start end A Min. : 1.000 Min. : 1 Min. : 735239 Min. :1 1st Qu.: 4.000 1st Qu.: 50450954 1st Qu.: 62622068 1st Qu.:1 Median : 9.000 Median :119502574 Median :131407920 Median :1 Mean : 9.932 Mean :116322448 Mean :130299118 Mean :1 3rd Qu.:15.000 3rd Qu.:182373738 3rd Qu.:195047428 3rd Qu.:1 Max. :24.000 Max. :248463057 Max. :249250621 Max. :1 B seg parent.index Min. :1 Min. : 1.0 Min. : NA 1st Qu.:1 1st Qu.:107.8 1st Qu.: NA Median :1 Median :214.5 Median : NA Mean :1 Mean :214.5 Mean :NaN 3rd Qu.:1 3rd Qu.:321.2 3rd Qu.: NA Max. :1 Max. :428.0 Max. : NA NA's :428 > summary(clone$seq) # this looks like a bug to me. Mode NA's logical 1 > > ### CNV and Mutations, without normal contamination > tumor <- Tumor(psis, rounds = 400, nu = 100, pcnv = 0.5, norm.contam = FALSE) > clone <- getClone(tumor, 1) > summary(clone$cn) chr start end A Min. : 1.000 Min. : 1 Min. : 1169759 Min. :1.000 1st Qu.: 4.000 1st Qu.: 47981792 1st Qu.: 57606017 1st Qu.:1.000 Median : 8.000 Median :105475912 Median :116363304 Median :1.000 Mean : 9.577 Mean :110576309 Mean :124049314 Mean :1.005 3rd Qu.:14.250 3rd Qu.:176042343 3rd Qu.:192224306 3rd Qu.:1.000 Max. :24.000 Max. :248849703 Max. :249250621 Max. :2.000 B seg parent.index Min. :1 Min. : 1.0 Min. :129 1st Qu.:1 1st Qu.:111.8 1st Qu.:129 Median :1 Median :222.5 Median :129 Mean :1 Mean :222.5 Mean :129 3rd Qu.:1 3rd Qu.:333.2 3rd Qu.:129 Max. :1 Max. :444.0 Max. :129 > summary(clone$seq) chr start seg mut.id Min. : 1.000 Min. : 238961 Min. : 1.0 Min. : 843 1st Qu.: 4.000 1st Qu.: 30715213 1st Qu.:118.2 1st Qu.: 2243 Median : 8.000 Median : 69051420 Median :217.5 Median :13386 Mean : 9.395 Mean : 76810967 Mean :219.6 Mean :15462 3rd Qu.:14.000 3rd Qu.:110514452 3rd Qu.:327.0 3rd Qu.:33403 Max. :24.000 Max. :245436242 Max. :438.0 Max. :33507 mutated.copies allele normal.copies Min. :1 A:199 Min. :1.000 1st Qu.:1 B:219 1st Qu.:1.000 Median :1 Median :1.000 Mean :1 Mean :1.005 3rd Qu.:1 3rd Qu.:1.000 Max. :1 Max. :2.000 > > ### CNV and Mutations, with normal contamination > tumor <- Tumor(psis, rounds = 400, nu = 100, pcnv = 0.5, norm.contam = TRUE) > clone <- getClone(tumor, 1) > summary(clone$cn) chr start end A Min. : 1.00 Min. : 1 Min. : 1993994 Min. :1 1st Qu.: 4.00 1st Qu.: 44864382 1st Qu.: 65814196 1st Qu.:1 Median : 8.00 Median :107677429 Median :127218534 Median :1 Mean : 9.83 Mean :110897887 Mean :132024871 Mean :1 3rd Qu.:15.00 3rd Qu.:176034854 3rd Qu.:205266052 3rd Qu.:1 Max. :24.00 Max. :248784714 Max. :249250621 Max. :1 B seg parent.index Min. :1 Min. : 1.00 Min. : NA 1st Qu.:1 1st Qu.: 71.25 1st Qu.: NA Median :1 Median :141.50 Median : NA Mean :1 Mean :141.50 Mean :NaN 3rd Qu.:1 3rd Qu.:211.75 3rd Qu.: NA Max. :1 Max. :282.00 Max. : NA NA's :282 > summary(clone$seq) # this looks like a bug to me. Mode NA's logical 1 > > ### CNV-only, with normal contamination > tumor <- Tumor(psis, rounds = 400, nu = 0, pcnv = 1, norm.contam = TRUE) > clone <- getClone(tumor, 1) > summary(clone$cn) chr start end A Min. : 1.000 Min. : 1 Min. : 967296 Min. :1 1st Qu.: 4.000 1st Qu.: 51624945 1st Qu.: 67372594 1st Qu.:1 Median : 8.000 Median :116311115 Median :131768014 Median :1 Mean : 9.797 Mean :115891630 Mean :133485790 Mean :1 3rd Qu.:15.000 3rd Qu.:173938834 3rd Qu.:200532361 3rd Qu.:1 Max. :24.000 Max. :248551840 Max. :249250621 Max. :1 B seg parent.index Min. :1 Min. : 1.00 Min. : NA 1st Qu.:1 1st Qu.: 85.75 1st Qu.: NA Median :1 Median :170.50 Median : NA Mean :1 Mean :170.50 Mean :NaN 3rd Qu.:1 3rd Qu.:255.25 3rd Qu.: NA Max. :1 Max. :340.00 Max. : NA NA's :340 > summary(clone$seq) # this is correct Length Class Mode 0 NULL NULL > > ### CNV-only, without normal contamination > tumor <- Tumor(psis, rounds = 400, nu = 0, pcnv = 1, norm.contam = FALSE) > clone <- getClone(tumor, 1) > summary(clone$cn) chr start end A Min. : 1.000 Min. : 1 Min. : 138132 Min. :0.000 1st Qu.: 4.000 1st Qu.: 55591968 1st Qu.: 69264028 1st Qu.:1.000 Median : 9.000 Median :116940858 Median :133942632 Median :1.000 Mean : 9.672 Mean :118481804 Mean :135380150 Mean :1.006 3rd Qu.:14.000 3rd Qu.:187725414 3rd Qu.:207668539 3rd Qu.:1.000 Max. :24.000 Max. :248140309 Max. :249250621 Max. :2.000 B seg parent.index Min. :0.000 Min. : 1.00 Min. :248 1st Qu.:1.000 1st Qu.: 89.25 1st Qu.:248 Median :1.000 Median :177.50 Median :248 Mean :1.003 Mean :177.50 Mean :248 3rd Qu.:1.000 3rd Qu.:265.75 3rd Qu.:248 Max. :2.000 Max. :354.00 Max. :248 > summary(clone$seq) # this is correct Length Class Mode 0 NULL NULL > > ### Test coercion routines > tumor <- as(tumor, "list") > object <- as(tumor, "Tumor") > > ### Test data generation (i.e., simulation) > dataset <- generateTumorData(object, + dataPars$snps.seq, dataPars$snps.cgh, dataPars$mu, + dataPars$sigma.reads, dataPars$sigma0.lrr, + dataPars$sigma0.baf, dataPars$density.sigma) > class(dataset) [1] "list" > length(dataset) [1] 2 > names(dataset) [1] "cn.data" "seq.data" > lapply(dataset, class) $cn.data [1] "data.frame" $seq.data [1] "data.frame" > lapply(dataset, dim) $cn.data [1] 354 7 $seq.data [1] 1000000 8 > summary(as.matrix(dataset$cn.data), digits = 3) chr seg LRR BAF Min. : 1.00 Min. : 1.0 Min. :-0.155351 Min. :0.286 1st Qu.: 4.00 1st Qu.: 89.2 1st Qu.:-0.002416 1st Qu.:0.499 Median : 9.00 Median :177.5 Median : 0.000553 Median :0.500 Mean : 9.67 Mean :177.5 Mean : 0.000868 Mean :0.499 3rd Qu.:14.00 3rd Qu.:265.8 3rd Qu.: 0.002919 3rd Qu.:0.501 Max. :24.00 Max. :354.0 Max. : 0.119217 Max. :0.714 X Y markers Min. :0.400 Min. :0.404 Min. : 832 1st Qu.:0.994 1st Qu.:0.994 1st Qu.:1459 Median :1.001 Median :1.001 Median :1698 Mean :1.002 Mean :1.004 Mean :1695 3rd Qu.:1.007 3rd Qu.:1.007 3rd Qu.:1920 Max. :1.594 Max. :1.620 Max. :2714 > summary(dataset$seq.data[,-(6:7)]) # note that all mut.id are NA's since there were no mutations chr seg mut.id refCounts Min. : 1.000 Min. : 1.0 Min. : NA Min. : 10.00 1st Qu.: 4.000 1st Qu.: 88.0 1st Qu.: NA 1st Qu.: 60.00 Median : 9.000 Median :177.0 Median : NA Median : 70.00 Mean : 9.638 Mean :177.1 Mean :NaN Mean : 69.71 3rd Qu.:14.000 3rd Qu.:265.0 3rd Qu.: NA 3rd Qu.: 79.00 Max. :24.000 Max. :354.0 Max. : NA Max. :148.00 NA's :1e+06 varCounts status Min. : 12.00 Length:1000000 1st Qu.: 61.00 Class :character Median : 70.00 Mode :character Mean : 70.24 3rd Qu.: 80.00 Max. :170.00 > > plotTumorData(object, dataset) > > > proc.time() user system elapsed 24.59 2.31 26.95