readBAM: pull in (filter and assemble as an object) some or all of the...

In biobenkj/complexion: Compute library complexity measures from sequencing data

Description

pull in (filter and assemble as an object) some or all of the "useful" reads in a paired-end sequencing run

Usage

readBAM(
  bam,
  genome = c("hg19", "hg38", "mm10", "mm9"),
  is.single = FALSE,
  bamParams = NULL,
  which = NULL,
  style = "UCSC",
  strand = c("unstranded", "forward", "reverse"),
  ...
)

Arguments

bam	character string, the BAM file to parse
genome	optional character string, the genome assembly to target
is.single	whethr the input BAM is single-end or not
bamParams	optional any parameters to pass through to ScanBamParam
which	optional a GRanges object with specific regions to extract
style	what style the assembly annotations are in (e.g. 'chr1' == UCSC or '1' == NCBI)
strand	what orientation is the first read in the pair (e.g. 'reverse')

Value

a GenomicAlignmentPairs object

biobenkj/complexion documentation built on June 25, 2020, 12:02 a.m.