R Under development (unstable) (2024-01-29 r85841 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
> niterboot <- 25
> # niterboot <- 250
> 
> if (visualize)
+ {
+   datafilename <- system.file("extdata", "transcripto_very_small_sample.txt", package="DRomics")
+   # to test the multi-page of plotfit2pdf take the file below
+   # datafilename <- system.file("extdata", "transcripto_sample.txt", package="DRomics")
+   o <- microarraydata(datafilename, check = TRUE, norm.method = "cyclicloess")
+   s <- itemselect(o) 
+   f <- drcfit(s)
+   r <- bmdcalc(f)
+   b <- bmdboot(r, niter = niterboot)
+   plot(f , BMDoutput = r, BMDtype = "zSD") 
+   plot(f , BMDoutput = b, BMDtype = "zSD") 
+   plot(f , BMDoutput = r, BMDtype = "xfold") 
+   plot(f , BMDoutput = b, BMDtype = "xfold") 
+   plot(f , items = 3,  BMDoutput = b, BMDtype = "zSD") 
+   plot(f , items = 6, BMDoutput = b,  BMDtype = "zSD") 
+   plot(f , items = c("12.1", "4", "70"),  BMDoutput = b, BMDtype = "zSD")
+   
+   plotfit2pdf(f , BMDoutput = r, BMDtype = "zSD") 
+   plotfit2pdf(f , BMDoutput = b, BMDtype = "zSD") 
+   plotfit2pdf(f , BMDoutput = r, BMDtype = "xfold") 
+   plotfit2pdf(f , BMDoutput = b, BMDtype = "xfold") 
+   plotfit2pdf(f , items = 3,  BMDoutput = r, BMDtype = "zSD") 
+   plotfit2pdf(f , items = 6, BMDoutput = b,  BMDtype = "xfold") 
+   plotfit2pdf(f , items = c("12.1", "4", "70"),  BMDoutput = r, BMDtype = "zSD") 
+   
+   
+   # Metabolo ex. case where there is a pb of items ordering 
+   datafilename <- system.file("extdata", "metabolo_sample.txt", package="DRomics")
+   o <- continuousomicdata(datafilename, backgrounddose = 0, check = TRUE)
+   s <- itemselect(o, select.method = 'quadratic', FDR = 0.05)
+   f <- drcfit(s, progressbar = FALSE, parallel = 'no')
+   plot(f, plot.type = 'dose_fitted', dose_log_transfo = TRUE)
+   r <- bmdcalc(f, z = 1, x = 10)
+   plot(f, plot.type = 'dose_fitted', BMDoutput = r, BMDtype = 'zSD', dose_log_transfo = TRUE) # good order
+   plotfit2pdf(f) # good order - initial order by p-value of the selection
+   plotfit2pdf(f , BMDoutput = r, BMDtype = "zSD")  # alphabetic order WHY ???????????????
+   b <- bmdboot(r, niter = 10)
+   plotfit2pdf(f , BMDoutput = b, BMDtype = "zSD") # alphabetic order
+ }
> 
> 
> proc.time()
   user  system elapsed 
   9.34    0.78   10.11