apex (version 1.0.2)

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, ...)
"concatenate"(x, genes = TRUE, ...)
"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.

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))

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