concatenate: Concatenate genes into a single matrix

In apex: Phylogenetic Methods for Multiple Gene Data

Description

These functions concatenate separate DNA alignments into a single alignement matrix. concatenate is a generic with methods for:

• multidna: returns a DNAbin matrix

• multiphyDat: returns a phyDat object

Usage

concatenate(x, ...)

## S4 method for signature 'multidna'
concatenate(x, genes = TRUE, ...)

## S4 method for signature 'multiphyDat'
concatenate(x, genes = TRUE, ...)

Arguments

x	a multidna or a multiphyDat object.
...	further arguments passed to other methods (currently not used).
genes	an optional vector indicating the genes to retain for the concatenation; any way to subset the list in x@dna is acceptable; by default, all genes are used.

Author(s)

Thibaut Jombart [e-mail]

Examples

## simple conversion with nicely ordered output
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
x
plot(x)

image(concatenate(x))

apex documentation built on April 14, 2020, 5:32 p.m.