inst/unitTests/test_general.R

In MPIIComputationalEpigenetics/WSHPackage: R package for the calculation of the following Within-Sample Heterogeneity Scores in Bisulfite Sequencing Data: FDRP, qFDRP, PDR, Epipolymorphism, Methylation Entropy and MHL

##' unit testing for WSH R package

##' checks if the example is correctly working
#test.example <- function(){
#  qfdrp <- wsh.run.example()$qFDRP
#  fdrp <- wsh.run.example("fdrp")$FDRP
#  pdr <- wsh.run.example("pdr")$PDR
#  #mhl <- wsh.run.example("mhl")
#  epipoly <- tryCatch(wsh.run.example("epipolymorphism")$Epipolymorphism,error=function(e){
#    if(Sys.info()['sysname']=="Windows"){
#     return(0)
#    }
#  })
#  entropy <- tryCatch(wsh.run.example("entropy")$Entropy,error=function(e){
#    if(Sys.info()['sysname']=="Windows"){
#      return(0)
#    }
#  })
#  passes <- is.numeric(qfdrp)&is.numeric(fdrp)&is.numeric(pdr)&is.numeric(epipoly)&is.numeric(entropy)
#  checkTrue(passes)
#}

##' tests function to compute WSH scores from GRanges objects
#test.GRanges <- function(){
#  example.bam <- system.file(file.path("extData","small_example.bam"),package="WSH")
#  example.GRanges <- GRanges(Rle(rep("chr2",10)),IRanges(start = c(2298361,2298554,2298732,2298743,2298787,2298792,2298827,2298884,
#                                                                   2298915,2298921),end=c(2298361,2298554,2298732,2298743,2298787,
#                                                                                          2298792,2298827,2298884,2298915,2298921)+1))
#  qfdrp <- compute.score(example.bam,example.GRanges,use.sex.chromosomes = T)
#  passes <- is.numeric(qfdrp$qFDRP)
#  checkTrue(passes)
#}

##' #' tests function to compute WSH scores from RnBSet objects
# test.rnbSet <- function(){
#  example.bam <- system.file(file.path("extData","small_example.bam"),package="WSH")
#  example.rnb.set <- system.file(file.path("extData","small_rnbSet.zip"),package="WSH")
#  pdr <- compute.score(example.bam,example.rnb.set,score="pdr")
#  passes <- is.numeric(pdr$PDR)
#  checkTrue(passes)
# }

#test.options <- function(){
#  names.new.options <- c("window.size","mapq.filter","max.reads","min.overlap","fdrp.type","coverage.threshold",
#                         "methclone.methylation.diff")
#  new.options <- c(window.size=42,mapq.filter=5,max.reads=10,min.overlap=59,fdrp.type="qFDRP",coverage.threshold=5,
#                   methclone.methylation.diff=0)
#  set.option(window.size=42,mapq.filter=5,max.reads=10,min.overlap=59,fdrp.type="qFDRP",coverage.threshold=5,
#             methclone.methylation.diff=0)
#  package.options <- get.option(names.new.options)
#  passes <- all(package.options == new.options)
#  tryCatch(set.option(perl.path="foo"),error=function(e){
#    passes <- FALSE
#  })
#  tryCatch(set.option(samtools.path="foo"),error=function(e){
#    passes <- FALSE
#  })
#  checkTrue(passes)
#}

# test.option.influence <- function(){
#   example.bam <- system.file(file.path("extData","small_example.bam"),package="WSH")
#   example.rnb.set <- system.file(file.path("extData","small_rnbSet.zip"),package="WSH")
#   fdrp.default <- rnb.calculate.fdrp(example.rnb.set,example.bam)
#   set.option(coverage.threshold = 50)
#   fdrp.new <- rnb.calculate.fdrp(example.rnb.set,example.bam)
#   passes <- nrow(fdrp.default) != nrow(fdrp.new)
#   set.option(coverage.threshold = 10)
#   fdrp.new <- rnb.calculate.fdrp(example.rnb.set,example.bam)
#   passes <- passes & (nrow(fdrp.default)==nrow(fdrp.new))
#   set.option(mapq.filter = 0)
#   fdrp.new <- rnb.calculate.fdrp(example.rnb.set,example.bam)
#   passes <- passes & (any(fdrp.default$FDRP!=fdrp.new$FDRP))
#   checkTrue(passes)
# }

#test.genomebrowser <- function(){
#	qfdrp <- wsh.run.example()
#	create.genomebrowser.track(qfdrp)
#	create.genomebrowser.track(qfdrp,bin.width=NULL)
#	res <- readLines("Sample_qFDRP.bed")
#	unlink("Sample_qFDRP.bed")
#	passes <- length(res) > 0
#	checkTrue(passes)
#}

##' main testing function
#execute.unit.test <- function(){
#  require("RUnit")
#  logger.start("Unit testing")
#    logger.start("Test example")
#      test.example()
#    logger.completed()
#    logger.start("Test GRanges function")
#      test.GRanges()
#    logger.completed()
#    # Only test locally
#    # logger.start("Test RnBSet function")
#    #    test.rnbSet()
#    # logger.completed()
#    logger.start("Test package options")
#      test.options()
#    logger.completed()
#    # Only test locally
#    # logger.start("Test package option influence")
#    #   test.option.influence()
#    # logger.completed()
#	logger.start("Test Genome Browser conversion")
#		test.genomebrowser()
#	logger.completed()
#  logger.completed()
#}

#execute.unit.test()