tests/testthat/test_IPA_analysis.R

In APAlyzer: A toolkit for APA analysis using RNA-seq data

test_that("IPA_analysis works properly", {
	URL="https://github.com/RJWANGbioinfo/PAS_reference_RData/blob/master/"
	file="mm9_REF.RData"
	source_data(paste0(URL,file,"?raw=True"))
	dfIPA=dfIPA[which(dfIPA$Chrom=='chr19'),]
	dfLE=dfLE[which(dfLE$Chrom=='chr19'),]	
	library("TBX20BamSubset")
	library("Rsamtools")
	flsall = getBamFileList()
	IPA_OUTraw=PASEXP_IPA(dfIPA, dfLE, flsall[1:2], Strandtype="forward", nts=1)
	expect_true(median(IPA_OUTraw$SRR316185_IPA_RE,na.rm=TRUE)>=0)	
	expect_true(median(IPA_OUTraw$SRR316184_IPA_RE,na.rm=TRUE)>=0)
})