repeatMask {deepSNV} | R Documentation

## Mask homopolymeric repeats.

### Description

This function masks homopolymeric repeats longer than a given width. These are hot-spots of sequencing error and can confound the analysis.

### Usage

    repeatMask(x, ...)

    ## S4 method for signature 'DNAString'
    repeatMask(x, w=5, flank=TRUE)

    ## S4 method for signature 'deepSNV'
    repeatMask(x, w=5, flank=TRUE)

### Arguments

`x` | An object. Either a `deepSNV-class` object or a `DNAString` with the nucleotide sequence.
`...` | Additional param passed to specific methods
`w` | Integer. The minimal length at which repeats should be masked. Default `w=0`.
`flank` | Boolean. Indicates whether the sites adjacent to the repeat should also be masked.

### Value

A boolean vector where TRUE indicates a non-homopolymeric region.

### Author(s)

Moritz Gerstung

### Examples

    data(HIVmix)
    which(repeatMask(HIVmix))

[Package deepSNV version 1.40.0 Index]