galp2gal: Convert GAlignmentPairs to GAlignments
In yueli-compbio/RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Description Usage Arguments Details Value Author(s) References See Also Examples

Convert GAlignmentPairs to GAlignments using CIGAR to mark flanked portion of the pairs as 'N'.

1	galp2gal(galp)

galp

Each proper read pairs is combined into a single alignment record making use of the CIGAR flag ‘N’ to indicate the number of bases between the mate pairs (i.e., the difference between the start of the right mate pair and the end of the left mate pair). In other words, the paired-end alignments are treated as gapped alignments of long fragments. The function is used within getAlignGal but can be used as a stand-alone function as well.

gal

GAlignments object containing for each paired alignments a single alignment record.

Yue Li

P. Aboyoun, H. Pages and M. Lawrence. GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.

getAlignGal, combineAlignGals, readGAlignments, readGAlignmentPairs, import

library(Rsamtools)

extdata.dir <- system.file("extdata", package="RIPSeeker")

ex1_file <- list.files(extdata.dir, "ex1.bam", recursive=TRUE, full.names=TRUE)

galp <- readGAlignmentPairs(ex1_file, use.names=TRUE)

galp

gal <- galp2gal(galp)

gal