apex (version 1.0.4)

multiphyDat-class: multiphyDat: class for multiple gene data

Description

This formal (S4) class is identical to '>multidna, except that DNA sequences are stored using phyDat objects from the phangorn package. Sequences are stored as a (possibly named) list, with each element of the list being a separate DNA alignment stored as a phyDat object. The rows of the separate matrices all correspond to the same individuals, ordered identically.

Slots

seq

a list of phyDat objects; empty slot should be NULL

type

a character string indicating the type of the sequences stored: "DNA" for DNA sequences, "AA" for amino-acids.

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

Examples

# NOT RUN {
data(Laurasiatherian)

## empty object
new("multiphyDat")

## simple conversion with nicely ordered output
# }
# NOT RUN {
genes <- list(gene1=subset(Laurasiatherian,,1:1600, FALSE),
    gene2=subset(Laurasiatherian,,1601:3179, FALSE))
x <- new("multiphyDat", genes)
x
# }
# NOT RUN {
## trickier conversion with missing sequences / wrong order
genes <- list(gene1=subset(Laurasiatherian,1:40),
    gene2=subset(Laurasiatherian,8:47))
x <- new("multiphyDat", genes)
x

# }