countAllelesFromBam {AllelicImbalance} | R Documentation

## alleleCounts from bam file

### 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)

[Package AllelicImbalance version 1.30.0 Index]