countAllelesFromBam: alleleCounts from bam file

In AllelicImbalance: Investigates Allele Specific Expression

Description

count alleles before creating ASEse.

Usage

countAllelesFromBam(gr, ...)

## S4 method for signature 'GRanges'
countAllelesFromBam(
  gr,
  pathToDir,
  flag = NULL,
  scanBamFlag = NULL,
  return.class = "array",
  verbose = TRUE,
  ...
)

Arguments

gr	GRanges that contains SNPs of interest
...	arguments to pass on
pathToDir	path to directory of bam files
flag	specify one flag to use as filter, default is no filtering. allowed flags are 99, 147, 83 and 163
scanBamFlag	set a custom flag to use as filter
return.class	type of class for the returned object
verbose	makes funciton more talkative

Details

counts the alleles in a bam file based on GRanges positions.

Important excerpt from the details section of the internal applyPileups function: Regardless of 'param' values, the algorithm follows samtools by excluding reads flagged as unmapped, secondary, duplicate, or failing quality control.

Author(s)

Jesper R. Gadin

Examples

data(GRvariants)
gr <- GRvariants

##not run at the moment
#pathToDir <- system.file('inst/extdata/ERP000101_subset', package='AllelicImbalance')
#ar <- countAllelesFromBam(gr, pathToDir)

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.