getDefaultMapBiasExpMean: Map Bias

Description

an allele frequency array

Usage

getDefaultMapBiasExpMean(alleleCountList, ...)
getDefaultMapBiasExpMean3D(alleleCountList, ...)
"getDefaultMapBiasExpMean"(alleleCountList)
"getDefaultMapBiasExpMean3D"(alleleCountList)

Arguments

alleleCountList

A GRangesList object containing read information

...

parameters to pass on

Value

getDefaultMapBiasExpMean returns a matrix with a default expected mean of 0.5 for every element.

Details

This function will assume there is no bias that comes from the mapping of reads, and therefore create a matrix with expected frequency of 0.5 for each allele.

Examples

Run this code


#load example data
data(ASEset)
#access SnpAfList
alleleCountList <- alleleCounts(ASEset)
#get default map bias exp mean
matExpMean <- getDefaultMapBiasExpMean(alleleCountList)

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