inst/unitTests/test_general.R

In schmic05/WSH_package: 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()