convertGaps: Convert gap characters

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

Description

Convert gap characters in an alignemnt

Usage

convertGaps(file, output, formatin = "sequential", formatout = formatin,
  colsep = "", from = "?", to = "-", overwrite = FALSE, ...)

Arguments

file	path and file name of a DNA alignment
output	path and file name for the modified file
formatin	format of the input file (to be passed to read.dna).
formatout	format for the output file (to be passed to write.dna, by default the same as formatin).
colsep	argument to be passed to write.dna, character used to separate columns in DNA alignment (ape's default is a single space, here we override this to no character, i.e. colsep="").
from	character to be changed in alignment (default “?”)
to	new character to use in alignment (default “-”)
overwrite	if no output file is specified, and overwrite is TRUE, then the original file is overwritten.
...	additional arguments to be passed to write.dna.

Details

This function is intended to replace one type of gap character (e.g., ‘?’) into another (e.g., ‘-’).

Value

the name of the output file (invisibly).

Author(s)

Francois Michonneau

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