defaultMapBias {AllelicImbalance} | R Documentation

## Generate default mapbias from genotype

### Description

Create mapbias array from genotype matrix requires genotype information

### Usage

    defaultMapBias(x, ...)

    ## S4 method for signature 'ASEset'
    defaultMapBias(x, return.class = "array")

### Arguments

`x` | `ASEset` object
`...` | internal arguments
`return.class` | "array" or "ASEset"

### Details

Default mapbias will be 0.5 for bi-allelic snps and 1 for homozygots. For genotypes with NA, 0.5 will be placed on all four alleles. Therefore tri-allelic can not be used atm. Genotype information has to be placed in the genotype(x) assay.

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

    #load example data
    data(ASEset.sim)

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

[Package AllelicImbalance version 1.20.0 Index]