multiAllelicFilt {AllelicImbalance} | R Documentation

## multi-allelic filter methods

### 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)

[Package AllelicImbalance version 1.30.0 Index]