deepSNV (version 1.18.3)

repeatMask: 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, ...)
"repeatMask"(x, w=5, flank=TRUE)
"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.

Examples

data(HIVmix)
which(repeatMask(HIVmix))