AllelicImbalance (version 1.10.2)

multiAllelicFilt: multi-allelic filter methods

Description

filter on multiallelic snps

Usage

multiAllelicFilt(x, ...)
"multiAllelicFilt"(x, strand = "*", threshold.count.sample = 10, threshold.frequency = 0.1, filterOver = "eachSample")

Arguments

x

ASEset object

...

internal param

strand

strand to infer from

threshold.count.sample

least amount of counts to try to infer allele

threshold.frequency

least fraction to classify (see details)

filterOver

'eachSample' or 'allSamples'

Details

based on the allele counts for all four variants A, T, G and C and returns true if there is counts enough suggesting a third or more alleles. The sensitivity can be specified using 'threshold.count.sample' and 'threshold.frequency'.

Examples

#load example data
data(ASEset)
a <- ASEset

multiAllelicFilt(a)