AllelicImbalance (version 1.8.3)

genofilters: genotype filter methods

Description

useful genotype filters

filter on multiallelic snps

Arguments

x

ASEset object

source

'genotype' or 'alleleCounts'

x

ASEset object

strand

strand to infer from

inferOver

'eachSample' or 'allSamples'

threshold.count.sample

least amount of counts to try to infer allele

threshold.frequency

least fraction to classify (see details)

Details

hetFilt returns TRUE if the samples is heterozygote, based on stored genotype information present in the phase data.

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

genotype(a) <- inferGenotypes(a)
hets <- hetFilt(a)
#load example data
data(ASEset)
a <- ASEset

multiAllelicFilt(a)