checkDNA: Check a DNA alignment for missing data

Description Usage Arguments Details Value Author(s) Examples

View source: R/checkDNA.R

Description

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

Usage

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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 <[email protected]>

Examples

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boopsboops/spider documentation built on May 6, 2019, 8:49 a.m.