R Under development (unstable) (2024-01-23 r85822 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(DRomics)
Loading required package: limma
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


DRomics has been loaded.
!!!! IMPORTANT CHANGES IN DEFAULT PLOT ARGUMENTS !!!!
Now all the plot functions use by default a log10 scale
for dose and BMD values, except curvesplot(),
for which the use of a dose log scale requires the specification
by the user of a non null minimal value (xmin).
We also put the default value of the argument scaling at TRUE
in curvesplot() and bmdplotwithgradient(),
to focus on shapes of dose-responses rather than on their amplitude.

> visualize <- FALSE # put to TRUE for a manual check of plots
> doboot <- FALSE
> 
> 
> if(visualize) 
+ {
+   
+   # Impact of ratio2switchinlog and minBMD on a toy example  
+   #
+   # datafilename <- system.file("extdata", "transcripto_very_small_sample.txt", package="DRomics")
+   datafilename <- system.file("extdata", "transcripto_sample.txt", package="DRomics")
+   (o <- microarraydata(datafilename, check = TRUE, norm.method = "cyclicloess"))
+   (s_quad <- itemselect(o, select.method = "quadratic", FDR = 0.01))
+   (f <- drcfit(s_quad, progressbar = TRUE))
+   (r <- bmdcalc(f))
+   plot(r) 
+   r$res
+   (r <- bmdcalc(f, ratio2switchinlog = 1))
+   plot(r) 
+   (r <- bmdcalc(f, minBMD = 2))
+   plot(r) 
+   (r <- bmdcalc(f, minBMD = 2, ratio2switchinlog = 1))
+   plot(r)
+   
+   # check of defensive prog
+   # (r <- bmdcalc(f, minBMD = 0))
+   # (r <- bmdcalc(f, minBMD = 1)) # 1 > minimal non null dose
+   
+   
+   # look at BMR in the output
+   (r <- bmdcalc(f, z = 2, x = 20))
+   r$res
+   r$minBMD
+   
+   # bootstrap after forcing minBMD to a high value
+   # without anay interest, but just to test bmdboot
+   (r <- bmdcalc(f, minBMD = 2))
+   (b <- bmdboot(r, niter = 100)) # with a non reasonable value for niter 
+   b$res
+   plot(b) # plot of BMD.zSD after removing of BMDs with infinite upper bounds
+   
+   # and with minBMD to its default value (dosemin/100)
+   (r <- bmdcalc(f))
+   (b <- bmdboot(r, niter = 100)) # with a non reasonable value for niter 
+   plot(b) # plot of BMD.zSD after removing of BMDs with infinite upper bounds
+   
+ 
+   # using an RNAseq example
+   # subsample
+   # datafilename <- system.file("extdata", "RNAseq_sample.txt", package="DRomics")
+   # (o <- RNAseqdata(datafilename, check = TRUE, transfo.method = "vst"))
+   
+   # whole data
+   data(Zhou_kidney_pce)
+   d <- Zhou_kidney_pce
+   (o <- RNAseqdata(d))
+   
+   (s <- itemselect(o, select.method = "quadratic", FDR = 0.01))
+   (f <- drcfit(s, progressbar = TRUE))
+   head(f$fitres)
+   
+   (r <- bmdcalc(f))
+   plot(r)
+   (r <- bmdcalc(f, ratio2switchinlog = 1))
+   plot(r) 
+   (r <- bmdcalc(f, minBMD = 0.0001, ratio2switchinlog = 1))
+   plot(r) 
+   (r <- bmdcalc(f, minBMD = 1))
+   plot(r) 
+ }
> 
> proc.time()
   user  system elapsed 
   9.32    0.73   10.03