| initialize,multiphyDat-method {apex} | R Documentation |
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 signature 'multiphyDat'
initialize(.Object, seq = NULL,
type = character(0), ind.info = NULL, gene.info = NULL,
add.gaps = TRUE, quiet = FALSE, ...)
Arguments
.Object |
the object skeleton, automatically generated when calling |
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 |
Value
an object of class multiphyDat containing alignments.
Author(s)
Klaus Schliep klaus.schliep@gmail.com
Thibaut Jombart t.jombart@imperial.ac.uk
See Also
the multiphyDat class
Examples
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