tests/testthat/test-methMatrixManipulation.R

In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices

context("test matrix manipulation")

testthat::test_that("getRelativeCoord orders columns correctly", {
  tss=33450
  dataMatrix<-matrix(c(1,1,0,0,0,1,1,0,0,0,0,0),nrow=3)
  colnames(dataMatrix)<-c(-200,-100,150,230)+tss
  regionGR<-GenomicRanges::GRanges(seqnames=c("chrI"),
                                  ranges=IRanges::IRanges(start=tss-250,
                                                          end=tss+250),
                                  strand="-")
  relMat<-getRelativeCoord(dataMatrix, regionGR,
                           invert=ifelse(GenomicRanges::strand(regionGR)=="+",
                                         F, T))
  testthat::expect_equal(as.numeric(colnames(relMat)),c(20,100,350,450))
})


testthat::test_that("getRelativeCoord orders columns correctly", {
  tss=33450
  dataMatrix<-matrix(c(1,1,0,0,0,1,1,0,0,0,0,0),nrow=3)
  colnames(dataMatrix)<-c(-200,-100,150,230)+tss
  regionGR<-GenomicRanges::GRanges(seqnames=c("chrI"),
                                   ranges=IRanges::IRanges(start=tss-250,
                                                           end=tss+250),
                                   strand="-")
  relMat<-getRelativeCoord(dataMatrix, regionGR,
                           invert=ifelse(GenomicRanges::strand(regionGR)=="+",
                                         F, T))
  testthat::expect_equal(as.numeric(colnames(relMat)),c(20,100,350,450))
})




# testthat::test_that("getMatrices subsets the matrix table correctly", {
#   #tss=33450
#   # read in the table with the list of matrix files
#   matTableFile<-system.file("extdata", "csv/MatrixLog_relCoord_ampTSS.csv",
#                             package="methMatrix", mustWork=TRUE)
#   matTable<-read.csv(matTableFile,stringsAsFactors=F)
#
#   # modify the matTable path to data
#   matTable$filename <-system.file("extdata", matTable[,"filename"],
#                                   package="methMatrix",
#                                   mustWork=TRUE)
#   # add matrices from another sample
#   matTable_dS03N2<-matTable
#   matTable_dS03N2$sample<-"dS03-N2"
#   matTable_dS03N2$filename<-gsub("dS02-182","dS03-N2",matTable$filename)
#
#   matTable<-rbind(matTable,matTable_dS03N2)
#
#   # read in the genomic ranges for TSSs
#   tssFile<-system.file("extdata","genome/ampliconMaxTSSgr.RDS",
#                        package="methMatrix",mustWork=TRUE)
#   tssWin<-readRDS(tssFile)
#   names(GenomicRanges::mcols(tssWin))<-"ID"
#   idx<-match(matTable$region,tssWin$ID)
#   tssWin<-tssWin[idx]
#   newMatList<-getMatrices(matTable,regionName=c("WBGene00015955","WBGene00009621"))
#   testthat::expect_equal(length(newMatList),dim(matTable)[1])
#   testthat::expect_equal(dim(newMatList[[3]])[1],matTable$fewNAreads[3])
# })
#


testthat::test_that("mergeSampleMats merges tables split by sample", {
  path=system.file("extdata","", package="methMatrix",mustWork=TRUE)
  regionType="rawAmp"
  samples=c("dS03-N2","dS03-N2")
  allMats<-mergeSampleMats(path, regionType, samples, deleteSplitFiles=F)
  testthat::expect_equal(nrow(allMats),8)
})