initialize,multiphyDat-method: multiphyDat constructor

Description

New multiphyDat objects can be created using new("multiphyDat", ...) where "..." are arguments documented below. The main input is a list of phyDat matrices. The constructor ensures that all matrices will be reordered in the same way, and genes with missing individuals will be filled by sequences of gaps ("-").

Usage

# S4 method for multiphyDat
initialize(.Object, seq = NULL,
  type = character(0), ind.info = NULL, gene.info = NULL,
  add.gaps = TRUE, quiet = FALSE, ...)

Value

an object of class multiphyDat containing alignments.

Arguments

.Object: the object skeleton, automatically generated when calling new.
seq: a list of phyDat matrices (1 per gene); rows should be labelled and indicate individuals, but different individuals and different orders can be used in different matrices.
type: a character string indicating the type of the sequences stored: "DNA" for DNA sequences, "AA" for amino-acids.
ind.info: an optional data.frame containing information on the individuals, where individuals are in rows.
gene.info: an optional data.frame containing information on the genes, where genes are in rows.
add.gaps: a logical indicating if gap-only sequences should be used where sequences are missing; defaults to TRUE.
quiet: a logical indicating if messages should be shown; defaults to FALSE.
...: further arguments to be passed to other methods

Author

Klaus Schliep klaus.schliep@gmail.com

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

Run this code

data(Laurasiatherian)
#' ## empty object
new("multiphyDat")

## simple conversion with nicely ordered output
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