checkAmbiguity: Check for ambiguities in a DNA sequence

In fmichonneau/chopper: Alignment Manipulations and Data Preparation for Phylogenetic Analyses

Description

Check for ambiguities or other characters that are not allowed in haplotypes.

Usage

checkAmbiguity(file, format = "fasta", quiet = FALSE, Namb = TRUE,
  simplify = TRUE, ...)

Arguments

file	path and file name for a DNA alignment (character)
format	format of the DNA alignment (passed to read.dna)
quiet	if FALSE, outputs as messages the ambiguities found (logical)
Namb	should Ns be considered ambiguities? (logical)
simplify	if TRUE, the returned object is reduced to only include the sequences that contain ambiguities. If FALSE, the returned object has the same length as the number of sequences in the alignment.
...	additional arguments to be passed to ape:::read.dna

Details

This function takes a DNA alignment and looks for characters in the sequence that are not A, C, T, G, -, ? (and optionally N). It ignores case.

Value

If there are no ambiguities, the function returns a zero-length integer vector. Otherwise, it returns a named list which includes for each sequence, the position in the alignment of the ambiguities for each sequence that has one or more ambiguities (if simplify=TRUE), and is named using the ambiguity. if quiet=FALSE, this vector is returned invisibly in addition of the

Author(s)

Francois Michonneau

fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.