inst/unitTests/test_methods.R

In easyRNASeq: Count summarization and normalization for RNA-Seq data

## to test the method result consistency over time
"test_simpleRNASeq" <- function(){

  ## datq directory
  tdir <- tutorialData()

  ## expected results
  columnSums <- c("ACACTG.bam" = 38381,
                  "ACTAGC.bam" = 28895,
                  "ATGGCT.bam" = 37569,
                  "TTGCGA.bam" = 41023)

  selectExons <- c("FBgn0003884:2"=1144,
                   "FBgn0003887:1"=1117,
                   "FBgn0038476:4"=850,
                   "FBgn0004867:1"=806,
                   "FBgn0037874:1"=709,
                   "FBgn0259745:6"=592)

  ## get the BamFileList
  filenames <- dir(tdir,pattern="[A,T].*\\.bam$",full.names=TRUE)
  indexnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData)
  bamFiles <- getBamFileList(filenames,indexnames)

  ## create the AnnotParam
  annotParam <- AnnotParam(fetchData("Dmel-mRNA-exon-r5.52.gff3.gz"))

  ## create the RnaSeqParam
  param <- RnaSeqParam(annotParam=annotParam,
                       bamParam=BamParam(paired=FALSE))

  ## get a RangedSummarizedExperiment containing the counts table
  sexp <- simpleRNASeq(
    bamFiles=bamFiles,
    param=param,
    verbose=FALSE
  )

  ## some cleanup needed because of the Bioc Cache
  colnames(sexp) <- sub(".*_","",colnames(sexp))
  sexp <- sexp[,order(colnames(sexp))]

  ## check the overall counts
  checkIdentical(colSums(assay(sexp)),columnSums)

  ## check the selected exon counts
  checkIdentical(head(sort(rowSums(assay(sexp))[rowSums(assay(sexp))>0],
                           decreasing=TRUE)),
                 selectExons)

}