consensusSequence-methods: Calculate the consensus sequence.

In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

Calculate the consensus sequence.

Description

This function computes the consensus sequence from a matrix of nucleotide counts, or the control slot of a deepSNV object.

Usage

consensusSequence(x, ...)

## S4 method for signature 'matrix'
consensusSequence(x, vector=FALSE, haploid=TRUE, het.cut = .333)

## S4 method for signature 'deepSNV'
consensusSequence(x, vector=FALSE, haploid=TRUE, het.cut = .333)

Arguments

x	An object. Either an deepSNV-class object, or a named matrix with nucleotide counts.
...	Additional arguments passed to methods.
vector	Boolean where TRUE indicates that a character vector should be returned.
haploid	Should the consensus be called for a haploid control? Otherwise, also all bases larger than het.cut are rerported. Default haploid = TRUE.
het.cut	Heterozygous cutoff. If haploid = FALSE, report all nucleotides with relative frequency larger than het.cut. Default = 0.333.

Value

A DNAString with the consensus sequence, or if vector = TRUE, a character vector.

Author(s)

Moritz Gerstung

Examples

data(HIVmix)
seq = consensusSequence(HIVmix)
consensusSequence(HIVmix, vector=TRUE)[1:10]

gerstung-lab/deepSNV documentation built on June 3, 2022, 3:05 p.m.