bamChrChunkApply: bamChrChunkApply

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

bamChrChunkApply

Description

Runs a function on reads/fragments from chunks of (chromosomes) of an indexed bam file. This is especially used by other functions to avoid loading all alignments into memory, or to parallelize reads processing.

Usage

bamChrChunkApply(
  x,
  FUN,
  paired = FALSE,
  keepSeqLvls = NULL,
  nChunks = 4,
  strandMode = 2,
  flgs = scanBamFlag(),
  exclude = NULL,
  mapqFilter = NA_integer_,
  BPPARAM = SerialParam(),
  ...
)

Arguments

x	A bam file.
FUN	The function to be run, the first argument of which should be a 'GRanges'
paired	Logical; whether to consider the reads as paired (fragments, rather than reads, will be returned)
keepSeqLvls	An optional vector of seqLevels to keep
nChunks	The number of chunks to use (higher will use less memory but increase overhead)
strandMode	Strandmode for paired data (see readGAlignmentPairs).
flgs	'scanBamFlag' for filtering the reads
exclude	An optional GRanges of regions for which overlapping reads should be excluded.
mapqFilter	Integer of the minimum mapping quality for reads to be included.
BPPARAM	A 'BiocParallel' parameter object for multithreading. Note that if used, memory usage will be high; in this context we recommend a high 'nChunks'.
...	Passed to 'FUN'

Value

A list of whatever 'FUN' returns

Examples

# as an example we'll use the function to obtain fragment sizes:
bam <- system.file("extdata", "ex1.bam", package="Rsamtools")
fragLen <- bamChrChunkApply(bam, paired=TRUE, FUN=function(x) width(x))
quantile(unlist(fragLen))

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.