apex (version 1.0.6)

concatenate: Concatenate genes into a single matrix

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

Thibaut Jombart

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))