refAllele {AllelicImbalance} | R Documentation

## Reference allele

### Description

Extract the allele based on SNP location from the reference fasta file

### Usage

    refAllele(x, fasta)

### Arguments

`x` | `ASEset` object
`fasta` | path to fasta file, index should be located in the same folder

### Details

The alleles will be placed in the rowRanges() meta column 'ref'

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

    #load example data
    data(ASEset.sim)

    fasta <- system.file('extdata/hg19.chr17.subset.fa', package='AllelicImbalance')
    a <- refAllele(ASEset.sim,fasta=fasta)

[Package AllelicImbalance version 1.25.2 Index]