getAlleleQuality {AllelicImbalance} | R Documentation

## snp quality data

### Description

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

### Usage

    getAlleleQuality(BamList, ...)

    ## S4 method for signature 'GAlignmentsList'
    getAlleleQuality(
      BamList,
      GRvariants,
      fastq.format = "illumina.1.8",
      return.class = "array",
      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.
`fastq.format` | default 'illumina.1.8'
`return.class` | 'list' or 'array'
`verbose` | Setting `verbose=TRUE` makes function more talkative

### Details

This function is used to retrieve the allele quality strings 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. The strand type information will be kept in the returned object. If the strand is marked as unknown "*", it will be forced to the "+" strand.

quaity information is extracted from the BamList object, and requires the presence of mcols(BamList)[["qual"]] to contain quality sequences.

### Value

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

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

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

    #get counts at the three positions specified in GRvariants
    alleleQualityArray <- getAlleleQuality(BamList=reads,GRvariants)

    #place in ASEset object
    alleleCountsArray <- getAlleleCounts(BamList=reads,GRvariants,
                         strand='*', return.class="array")

    	a <- ASEsetFromArrays(GRvariants, countsUnknown = alleleCountsArray)
    	aquals(a) <- alleleQualityArray

[Package AllelicImbalance version 1.32.0 Index]