bwGenomeCompatibility {CAGEfightR} | R Documentation |
Given a genome, checks whether a series of BigWig-files are compatible by checking if all common seqlevels have equal seqlengths.
bwGenomeCompatibility(plusStrand, minusStrand, genome)
plusStrand |
BigWigFileList: BigWig files with plus-strand CTSS data. |
minusStrand |
BigWigFileList: BigWig files with minus-strand CTSS data. |
genome |
Seqinfo: Genome information. |
TRUE, raises an error if the supplied genome is incompabtible.
Other BigWig functions:
bwCommonGenome()
,
bwValid()
if (.Platform$OS.type != "windows") { # Use the BigWig-files included with the package: data('exampleDesign') bw_plus <- system.file('extdata', exampleDesign$BigWigPlus, package = 'CAGEfightR') bw_minus <- system.file('extdata', exampleDesign$BigWigMinus, package = 'CAGEfightR') # Create two named BigWigFileList-objects: bw_plus <- BigWigFileList(bw_plus) bw_minus <- BigWigFileList(bw_minus) names(bw_plus) <- exampleDesign$Name names(bw_minus) <- exampleDesign$Name # Make a smaller genome: si <- seqinfo(bw_plus[[1]]) si <- si['chr18'] # Check if it is still compatible: bwGenomeCompatibility(plusStrand=bw_plus, minusStrand=bw_minus, genome=si) }