checkInternalGaps: Check for internal gaps in a DNA sequence.

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

Description

Check for internal gaps.

Usage

checkInternalGaps(file, format = "fasta", quiet = TRUE, ...)

Arguments

file	path and file name for a DNA alignment.
format	format of the DNA alignment.
quiet	if FALSE, outputs as messages the list of gaps found in the sequences.
...	additional arguments to be passed to ape:::read.dna

Details

This function takes a DNA alignment and looks for internal gaps (gaps in the middle of a sequence). For protein-coding DNA sequences, these indicate that the original file (e.g., trace files) need to be inspected closely.

Value

If there are no internal gaps, the function returns a zero-length integer vector. Otherwise, if quiet=TUE, the function returns a named vector that indicates the position in the alignment of the internal gaps for each sequence that has one or more internal gaps, if quiet=FALSE, this vector is returned invisibly in addition of the messages.

Author(s)

Francois Michonneau

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