consensusSeqs {CrispRVariants} | R Documentation

## Get consensus sequences for variant alleles

### Description

Return consensus sequences of variant alleles. At present, chimeric alignments are not included.

### Usage

    consensusSeqs(obj, ...)

    ## S4 method for signature 'CrisprSet'
    consensusSeqs(obj, ..., top.n = NULL, min.freq = 0,
      min.count = 1)

### Arguments

`obj` | An object containing aligned sequences
`...` | additional arguments
`top.n` | (Integer n) If specified, return variants ranked at least n according to frequency across all samples (Default: 0, i.e. no cutoff)
`min.freq` | (Float n least one sample (Default: 0)
`min.count` | (Integer n) Return variants with count greater than n in at least one sample (Default: 0)

### Value

A DNAStringSet of consensus sequences on the positive strand.

### Author(s)

Helen Lindsay

### Examples

    data("gol_clutch1")
    seqs <- consensusSeqs(gol, sample = 2)

[Package CrispRVariants version 1.15.0 Index]