defaultMapBias: Generate default mapbias from genotype

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

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) 

pappewaio/AllelicImbalance documentation built on April 11, 2020, 2:58 a.m.