is.ambig: Missing bases in alignments

In spider: Species Identity and Evolution in R

Description

Checks what columns in an alignment have ambiguous bases or missing data.

Usage

is.ambig(DNAbin)

Arguments

DNAbin

A DNA alignment of class ‘DNAbin’.

Details

Ambiguous bases are bases that have been coded with any of the Union of Pure and Applied Chemistry (IUPAC) DNA codes that are not A, C, G, or T. Missing data are bases that have been coded with "-", "?" or "N".

Value

A logical vector containing TRUE if ambiguous bases or missing data are present, FALSE if not. Does not differentiate between the two classes of data.

Author(s)

Samuel Brown <[e-mail]>

See Also

checkDNA

Examples

data(woodmouse)
is.ambig(woodmouse)
#Columns with ambiguous bases
which(is.ambig(woodmouse))

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