addPseudoAlignment {RIPSeeker} | R Documentation |
Check whether chromosome has at least one alignment to prevent abnormal behaviour of the subsequent functions. In case no alignment is found on an entire chromosome, add a pseudo-alignment as a placeholder for that chromosome.
addPseudoAlignment(alignGR)
alignGR |
GRanges object containing the alignment information. |
In case no alignment is found on an entire chromosome, add an alignment with start 1 and end 20 as a placeholder for the chromosome. This step is necessary to maintian the chromosome information.
alignGR |
Original or augmented input GRanges object with pseudoreads, depending on whether there exists empty chromosome(s). |
Yue Li
combineAlignGals, readGAlignments, readGAlignmentPairs, import
# Retrieve system files extdata.dir <- system.file("extdata", package="RIPSeeker") bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE) bamFiles <- grep("PRC2", bamFiles, value=TRUE) alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9") alignGR <- as(alignGal, "GRanges") alignGR x <- addPseudoAlignment(alignGR) x