multiphyDat-class | R Documentation |
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.
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
Klaus Schliep klaus.schliep@gmail.com
Thibaut Jombart t.jombart@imperial.ac.uk
data(Laurasiatherian)
## empty object
new("multiphyDat")
## simple conversion with nicely ordered output
data(Laurasiatherian)
genes <- list(gene1=Laurasiatherian[, 1:1600],
gene2=Laurasiatherian[, 1601:3179])
x <- new("multiphyDat", genes)
x
## trickier conversion with missing sequences / wrong order
genes <- list(gene1=Laurasiatherian[1:40,],
gene2=Laurasiatherian[8:47,])
x <- new("multiphyDat", genes)
x
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