repeatMask-methods: Mask homopolymeric repeats.

In deepSNV: Detection of subclonal SNVs in deep sequencing data.

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))

deepSNV documentation built on Nov. 8, 2020, 8:01 p.m.