addPseudoAlignment: Add a psuedoalignment as a placeholder for the chromosome...

In RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

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.

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.

Value

alignGR

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

Author(s)

Yue Li

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

RIPSeeker documentation built on Oct. 31, 2019, 7:29 a.m.