R Under development (unstable) (2024-01-29 r85841 ucrt) -- "Unsuffered Consequences"
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> # Test DRomics on datasets without replicates and without control data
> 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", "insitu_RNAseq_sample.txt", package="DRomics")
+   (o <- RNAseqdata(datafilename, backgrounddose = 2e-2, transfo.method = "vst"))
+ #  (o <- RNAseqdata(datafilename, backgrounddose = 2e-2, transfo.method = "rlog"))
+   (s <- itemselect(o)) 
+ #  (s <- itemselect(o, select.method = "ANOVA")) # should stop
+   (f <- drcfit(s))
+   (fbis <- drcfit(s, enablesfequal0inGP = FALSE,
+                   enablesfequal0inLGP = FALSE, 
+                   preventsfitsoutofrange = FALSE))
+   # Focus on eliminated curves (peak out of range)
+   (idnotinf <- fbis$fitres$id[!(fbis$fitres$id %in% f$fitres$id)])
+   plot(fbis, items = idnotinf, dose_log_transfo = TRUE)
+   plot(fbis, items = idnotinf, dose_log_transfo = FALSE)
+ 
+     # Focus on simplified biphasic models in monotonic models
+   (id2explore <- f$fitres$id[f$fitres$model %in% c("Gauss-probit", "log-Gauss-probit") & 
+                               f$fitres$f == 0])
+   f$fitres[f$fitres$id %in%  id2explore, ]
+   plot(f, items = id2explore, dose_log_transfo = TRUE)
+   plot(fbis, items = id2explore, dose_log_transfo = TRUE)
+   plot(f, items = id2explore, dose_log_transfo = FALSE)
+   plot(fbis, items = id2explore, dose_log_transfo = FALSE)
+   
+   (r <- bmdcalc(f))
+   (rbis <- bmdcalc(fbis))
+   b <- bmdboot(r, niter = niterboot)
+   bbis <- bmdboot(rbis, niter = niterboot)
+   
+   plot(f , items = id2explore,
+        BMDoutput = b, dose_log_transfo = TRUE) 
+   plot(fbis , items = id2explore, 
+        BMDoutput = bbis, dose_log_transfo = TRUE) 
+ 
+ }
> 
> proc.time()
   user  system elapsed 
   8.81    0.76    9.59