coverageBams: Coverage

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Coverage

Description

Calculate the breadth (fraction of the genome that is covered by reads) and depth (average number of times each position in the genome has been sequenced) of coverage from a set of BAM file(s) (see Molnar & Ilie (2015)). Results are identical to those from samtools depth.

Usage

coverageBams(
  bamFiles,
  yieldSize = 10^4,
  seq.ids = NULL,
  out.file = NULL,
  max.depth = 10^4,
  min.base.quality = 1,
  min.mapq = 5,
  min.nucleotide.depth = 1,
  distinguish.strands = FALSE,
  distinguish.nucleotides = FALSE,
  ignore.query.Ns = FALSE,
  include.deletions = FALSE,
  include.insertions = FALSE,
  is.paired = NA,
  is.proper.pair = NA,
  is.unmapped.query = FALSE,
  has.unmapped.mate = NA,
  is.minus.strand = NA,
  is.mate.minus.strand = NA,
  is.first.mate.read = NA,
  is.second.mate.read = NA,
  is.secondary.align = FALSE,
  is.not.passing.qc = FALSE,
  is.dupl = FALSE,
  verbose = 1,
  nb.cores = 1
)

Arguments

bamFiles	vector of paths to BAM file(s), each of them having an index file with the same name but finishing by ".bai"; if there are several BAM files, all of them should contain reads aligned on the same set of sequences (i.e. the same reference genome)
yieldSize	number of records to yield each time the file is read from (see BamFile)
seq.ids	sequence identifier(s) to focus on, e.g. "chr2" or c("chr2","chr5"); if NULL, all of them
out.file	if not NULL, the output will be transformed into a data.frame and written into the given file
max.depth	see PileupParam
min.base.quality	see PileupParam
min.mapq	see PileupParam
min.nucleotide.depth	see PileupParam
distinguish.strands	see PileupParam
distinguish.nucleotides	see PileupParam
ignore.query.Ns	see PileupParam
include.deletions	see PileupParam
include.insertions	see PileupParam
is.paired	see scanBamFlag
is.proper.pair	see scanBamFlag
is.unmapped.query	see scanBamFlag
has.unmapped.mate	see scanBamFlag
is.minus.strand	see scanBamFlag
is.mate.minus.strand	see scanBamFlag
is.first.mate.read	see scanBamFlag
is.second.mate.read	see scanBamFlag
is.secondary.align	see scanBamFlag
is.not.passing.qc	see scanBamFlag
is.dupl	see scanBamFlag
verbose	verbosity level (0/1/2)
nb.cores	the number of cores to use to parallelize over bamFiles, i.e. at most how many child processes will be run simultaneously (not on Windows)

Value

list with one component per BAM file, each being a matrix with columns "nb.bases", "mapped.bases", "count.sum", "breadth", "depth" and "depth.map" (corresponding to the depth at positions with at least one mapped read)

Author(s)

Timothee Flutre (with the help of Martin Morgan)

See Also

freadBedtoolsCoverageHist

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.