repeatMask-methods: Mask homopolymeric repeats.

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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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.

flank

Boolean. Indicates whether the sites adjacent to the repeat should also be masked.

w

Integer. The minimal length at which repeats should be masked. Default w=0.

...

Additional param passed to specific methods

Value

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

Author(s)

Moritz Gerstung

Examples

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mg14/deepSNV-old documentation built on May 22, 2019, 8:52 p.m.