consensusSeqs: Get consensus sequences for variant alleles

In CrispRVariants: Tools for counting and visualising mutations in a target location

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)

CrispRVariants documentation built on Nov. 8, 2020, 11:09 p.m.