inst/unitTests/test_cexor.R

In pmb59/CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

test_cexor <- function() {

	owd <- setwd(tempdir())

	rep1 <- "CTCF_rep1_chr2_1-1e6.bam"
	rep2 <- "CTCF_rep2_chr2_1-1e6.bam"
	rep3 <- "CTCF_rep3_chr2_1-1e6.bam"

	r1 <- system.file( "extdata", rep1, package="CexoR",mustWork = TRUE )
	r2 <- system.file( "extdata", rep2, package="CexoR",mustWork = TRUE )
	r3 <- system.file( "extdata", rep3, package="CexoR",mustWork = TRUE )
	
	out <- cexor( bam=c(r1,r2,r3), chrN="chr2", chrL=1e6, N=3e4, p=1e-12 )

	# check that the example data outputs a GRanges with 13 ranges 
    	checkEquals( length(out$bindingEvents), 13 )

    	# check that if minimal input is not introduced the package recognizes an error situation
	# bam
	checkException( cexor(bam=c(), chrN="chr2", chrL=1e6, N=3e4) )
	# chrN
	checkException( cexor(bam=c(r1,r2,r3), chrN=c(), chrL=1e6, N=3e4) )
	# chrL
	checkException( cexor(bam=c(r1,r2,r3), chrN="chr2", chrL=c(), N=3e4) )

	setwd(owd)
}