initialize,multidna-method: multidna constructor

Description

New multidna objects can be created using new("multidna", ...) where "..." are arguments documented below. The main input is a list of DNAbin matrices. The constructor ensures that all matrices will be reordered in the same way, and as an option (setting add.gaps=TRUE, gap-only sequences ("...-----...") will be added wherever sequences are missing.

Usage

# S4 method for multidna
initialize(.Object, dna = NULL, ind.info = NULL,
  gene.info = NULL, add.gaps = TRUE, quiet = FALSE, ...)

Value

an object of class multidna containing alignments.

Arguments

.Object: the object skeleton, automatically generated when calling new.
dna: a list of DNAbin matrices (1 per gene); rows should be labelled and indicate individuals, but different individuals and different orders can be used in different matrices.
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

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

Run this code


## 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]])