getAlleleCounts {AllelicImbalance} | R Documentation

## snp count data

### Description

Given the positions of known SNPs, this function returns allele counts from a BamGRL object

### Usage

    getAlleleCounts(BamList, ...)

    ## S4 method for signature 'GAlignmentsList'
    getAlleleCounts(
      BamList,
      GRvariants,
      strand = "*",
      return.class = "list",
      verbose = TRUE,
      ...
    )

### Arguments

`BamList` | A `GAlignmentsList object` or `GRangesList object` containing data imported from a bam file
`...` | parameters to pass on
`GRvariants` | A `GRanges object` that contains positions of SNPs to retrieve
`strand` | A length 1 `character` with value '+', '-', or '*'. This argument determines if `getAlleleCounts` will retrieve counts from all reads, or only from reads marked as '+', '-' or '*' (unknown), respectively.
`return.class` | 'list' or 'array'
`verbose` | Setting `verbose=TRUE` makes function more talkative

### Details

This function is used to retrieve the allele counts from specified positions in a set of RNA-seq reads. The `BamList` argument will typically have been created using the `impBamGAL` function on bam-files. The `GRvariants` is either a GRanges with user-specified locations or else it is generated through scanning the same bam-files as in `BamList` for heterozygote locations (e.g. using `scanForHeterozygotes`). The GRvariants will currently only accept locations having width=1, corresponding to bi-allelic SNPs. In the `strand` argument, specifying '*' is the same as retrieving the sum count of '+' and '-' reads (and unknown strand reads in case these are found in the bam file). '*' is the default behaviour and can be used when the RNA-seq experiments strand information is not available.

### Value

`getAlleleCounts` returns a list of several data.frame objects, each storing the count data for one SNP.

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### See Also

- The `scanForHeterozygotes` which is a function to find possible heterozygote sites in a GenomicAlignments object

### Examples

    #load example data
    data(reads)
    data(GRvariants)

    #get counts at the three positions specified in GRvariants
    alleleCount <- getAlleleCounts(BamList=reads,GRvariants,
    strand='*')

    #if the reads had contained stranded data, these two calls would
    #have given the correct input objects for getAlleleCounts
    alleleCountPlus <- getAlleleCounts(BamList=reads,GRvariants,
    strand='+')
    alleleCountMinus <- getAlleleCounts(BamList=reads,GRvariants,
    strand='-')

[Package AllelicImbalance version 1.25.2 Index]