prepIgBam: Extract alignments in intergenic regions from BAM files

Description Usage Arguments Value Examples

View source: R/prepIgBam.R

Description

Extract alignments in intergenic regions from BAM files

Usage

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prepIgBam(finbam, iggrs, foutbam, max_uni_n_dup_aln = 10,
    max_mul_n_dup_aln = 10)

Arguments

finbam

Full name of an input RNA-seq BAM file. Currently, PRAM only supports strand-specific paired-end data with the first mate on the right-most of transcript coordinate, i.e., 'fr-firststrand' by Cufflinks's definition

iggrs

A GenomicRanges object defining intergenic regions

foutbam

Full name of an output BAM file to save all alignment fell into intergenic regions

max_uni_n_dup_aln

Maximum number of uniquely mapped fragments to report per each alignment. Default: 10

max_mul_n_dup_aln

Maximum number of multi-mapping fragments to report per each alignment. Default: 10

Value

None

Examples

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finbam = system.file('extdata/bam/CMPRep2.sortedByCoord.raw.bam',
                    package='pram')

iggrs = GenomicRanges::GRanges('chr10:77236000-77247000:+')

foutbam = tempfile(fileext='.bam')


prepIgBam(finbam, iggrs, foutbam)

pram documentation built on Nov. 8, 2020, 11:08 p.m.