AllelicImbalance (version 1.10.2)

inferAlleles: inference of SNPs of ASEset

Description

inference of SNPs

Usage

inferAlleles(x, strand = "*", return.type = "bi", threshold.frequency = 0, threshold.count.sample = 1, inferOver = "eachSample", allow.NA = FALSE)

Arguments

x

ASEset

strand

strand to infer from

return.type

'uni' 'bi' 'tri' 'quad' 'all'

threshold.frequency

least fraction to classify (see details)

threshold.count.sample

least amount of counts to try to infer allele

inferOver

'eachSample' or 'allSamples'

allow.NA

treat NA as zero when TRUE

Details

threshold.frequency is the least fraction needed to classify as bi tri or quad allelic SNPs. If 'all' then all of bi tri and quad allelic SNPs will use the same threshold. Everything under the treshold will be regarded as noise. 'all' will return a matrix with snps as rows and uni bi tri and quad will be columns. For this function Anything that will return TRUE for tri-allelicwill also return TRUE for uni and bi-allelic for the same SNP an Sample.

Examples

data(ASEset)
i <- inferAlleles(ASEset)