multidna: multidna: class for multiple gene data

In apex: Phylogenetic Methods for Multiple Gene Data

multidna: class for multiple gene data

Description

This formal (S4) class is used to store multiple DNA alignments. Sequences are stored as a (possibly named) list, with each element of the list being a separate DNA alignment stored as a DNAbin matrix. The rows of the separate matrices all correspond to the same individuals, ordered identically.

Slots

dna

a list of DNAbin matrices; empty slot should be NULL

labels

a vector of labels of individuals

n.ind

the number of individuals

n.seq

the total number of sequences (pooling all genes), including gap sequences

n.seq.miss

the total number of gap-only sequences

ind.info

a data.frame containing information on the individuals, where individuals are in rows; empty slot should be NULL

gene.info

a data.frame containing information on the genes, where genes are in rows; empty slot should be NULL

Author(s)

Thibaut Jombart [e-mail]

Examples

## empty object
new("multidna")

## simple conversion with nicely ordered output
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
x
image(woodmouse)
image(x@dna[[1]])
image(x@dna[[2]])

## trickier conversion with missing sequences / wrong order
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[c(5:1,14:15),501:965])
x <- new("multidna", genes)
x
image(x@dna[[1]])
image(x@dna[[2]])

apex documentation built on Aug. 8, 2025, 7:51 p.m.