multiAllelicFilt: multi-allelic filter methods

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

filter on multiallelic snps

Usage

multiAllelicFilt(x, ...)

## S4 method for signature 'ASEset'
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'.

Author(s)

Jesper R. Gadin, Lasse Folkersen

Examples

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

multiAllelicFilt(a)

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