subs-methods {haplotypes}

Displays base substitutions

Description

This function displays all base substitutions. If fifth=="TRUE", each gap is treated as a fifth state character.

Usage

## S4 method for signature 'Dna'
subs(x,fifth=FALSE)

Arguments

x

an object of class Dna.

fifth

boolean; should gaps be treated as a fifth state character?

Value

a list with three components:

subsmat:

a sequence matrix showing substitutions.

subs:

a list of matrices of the substitutions.

subsmnum:

total number of substitutions.

Methods

signature(x = "Dna")

Author(s)

Caner Aktas, [e-mail].

Examples

data("dna.obj")
x<-dna.obj

## Base substitutions.
subs(x)

## Gaps are treated as a fifth state character.
subs(x,fifth=TRUE)