bwCommonGenome {CAGEfightR} | R Documentation |
Finds a common genome for a series of BigWig-files, either using only levels present in all files (intersect) or in any file (union).
bwCommonGenome(plusStrand, minusStrand, method = "intersect")
plusStrand |
BigWigFileList: BigWig files with plus-strand CTSS data. |
minusStrand |
BigWigFileList: BigWig files with minus-strand CTSS data. |
method |
character: Either 'intersect' or 'union'. |
Sorted Seqinfo-object.
Other BigWig functions: bwGenomeCompatibility
,
bwValid
# 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 # Find the smallest common genome (intersect) across the BigWigList-objects: bwCommonGenome(plusStrand=bw_plus, minusStrand=bw_minus, method='intersect') # Find the most inclusive genome (union) across the BigWigList-objects: bwCommonGenome(plusStrand=bw_plus, minusStrand=bw_minus, method='union')