R Under development (unstable) (2024-01-23 r85822 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
> 
> if (visualize)
+ {
+   ## test of the selection step with limma
+   data(Scenedesmus_metab)
+   head(Scenedesmus_metab)
+   set.seed(1234)
+ 
+   # build of a dataset without 0 nor replicate
+   Scenedesmus_metab2 <- Scenedesmus_metab[, c(1,14:25)]
+   Scenedesmus_metab2[1, -1] <- Scenedesmus_metab2[1, -1] * runif(11, 0.9, 1.1)
+   head(Scenedesmus_metab2)
+   
+   (oerror <- continuousomicdata(Scenedesmus_metab2)) ## should stop with an explicite error message
+   
+   # build of a dataset without replicate but with at least a 0
+   Scenedesmus_metab2 <- Scenedesmus_metab[, c(1,14:25)]
+   Scenedesmus_metab2[1, -1] <- Scenedesmus_metab2[1, -1] * runif(11, 0.9, 1.1)
+   Scenedesmus_metab2[1, -1] <- Scenedesmus_metab2[1, -1]* (Scenedesmus_metab2[1, -1] > 1)
+   head(Scenedesmus_metab2)
+   
+   (o <- continuousomicdata(Scenedesmus_metab))
+   plot(o)
+   (s <- itemselect(o, select.method = "quadratic"))
+   (f <- drcfit(s))
+   plot(f)
+   
+   (o2 <- continuousomicdata(Scenedesmus_metab2))
+   plot(o2)
+   (s2 <- itemselect(o2, select.method = "quadratic"))
+   (f2 <- drcfit(s2))
+   plot(f2)
+   
+   ## Test of the selection step with DESeq2
+   data(Zhou_kidney_pce)
+   head(Zhou_kidney_pce)
+   Zhou <- Zhou_kidney_pce[1:1000, ]
+   
+   # build of a dataset without control nor replicate
+   Zhou2 <- Zhou[, c(1, 4:15)]
+   Zhou2[1, -1] <- Zhou2[1, -1] * runif(11, 0.9, 1.1)
+   head(Zhou2)
+   (oerror <- RNAseqdata(Zhou2))
+   
+   # build of a dataset without replicate
+   Zhou2 <- Zhou[, c(1, 4:15)]
+   Zhou2[1, -1] <- Zhou2[1, -1] * runif(11, 0.9, 1.1)
+   Zhou2[1, -1] <- Zhou2[1, -1] * (Zhou2[1, -1] > 0.3)
+   head(Zhou2)
+   (o <- RNAseqdata(Zhou))
+   plot(o)
+   (s <- itemselect(o, select.method = "quadratic"))
+   (f <- drcfit(s))
+   plot(f, dose_log_transfo = TRUE)
+   
+   (o2 <- RNAseqdata(Zhou2))
+   plot(o2)
+   (s2 <- itemselect(o2, select.method = "quadratic"))
+   (f2 <- drcfit(s2))
+   plot(f2, dose_log_transfo = TRUE)
+   
+ }
> 
> proc.time()
   user  system elapsed 
   8.00    0.85    8.82