combineAlignGals: Combine alignment files into a single GAlignments object
In yueli-compbio/RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

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

Import and process individual BAM/SAM/BED alignment files using getAlignGal and combine them into a single GAlignments.

1	combineAlignGals(bamFiles, ...)

`bamFiles`	A list of paths to the alignment files.
`...`	Arguments passed to `getAlignGal`.

If there is only one BAM file, then simply return the output from getAlignGal; otherwise, all processed alignments are pooled to form a single GAlignments object.

combinedGal

GAlignments object containning the (combined) processed alignments with the values slot saved for the "uniqueHits" binary flag defined in getAlignGal and metadata saved as a list containing argument setting for reverseComplement, returnDuplicate, flagMultiHits, returnOnlyUniqueHits defined in getAlignGal

User are recommanded to pool technical replicates but keep biological replicate separate for confirmation.

Yue Li

getAlignGal, 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)

# combine the alignments for technical replicates
alignGal <- 
combineAlignGals(bamFiles=grep(pattern="SRR039214", 
                  bamFiles, value=TRUE, invert=TRUE), 
                  reverseComplement=TRUE, genomeBuild="mm9")