RIPSeeker (version 1.12.0)

addPseudoAlignment: Add a psuedoalignment as a placeholder for the chromosome (Internal function)

Description

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.

Usage

addPseudoAlignment(alignGR)

Arguments

alignGR

GRanges object containing the alignment information.

Value

• alignGR
  Original or augmented input GRanges object with pseudoreads, depending on whether there exists empty chromosome(s).

Details

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.

See Also

combineAlignGals, readGAlignments, readGAlignmentPairs, import

Examples

# 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