checkDNA: Check a DNA alignment for missing data

In spider: Species Identity and Evolution in R

Description

This functions counts the number of bases in an alignment that are composed of missing data.

Usage

checkDNA(DNAbin, gapsAsMissing = TRUE)

Arguments

DNAbin	A DNA alignment of class ‘DNAbin’.
gapsAsMissing	Logical. Should gaps (coded as '-') be considered missing bases? Default of TRUE.

Details

This function considers bases coded as '?' and 'N' as missing data. By default, gaps (coded as '-') are also considered missing.

Value

A numeric vector giving the number of missing bases in each sequence of the alignment.

Author(s)

Samuel Brown <[e-mail]>

Examples

data(anoteropsis)
checkDNA(anoteropsis)
checkDNA(anoteropsis, gapsAsMissing=FALSE)

spider documentation built on May 2, 2019, 5:16 p.m.