| as.genlight {adegenet} | R Documentation |
Conversion to class "genlight"
Description
The class genlight is a formal (S4) class for storing a genotypes
of binary SNPs in a compact way, using a bit-level coding scheme. New
instances of this class are best created using new; see the
manpage of genlight for more information on this point.
As a shortcut, conversion methods can be used to convert various
objects into a genlight object. Conversions can be
achieved using S3-style (as.genlight(x)) or S4-style
(as(x,"genlight") procedures. All of them call upon the
constructor (new) of genlight objects.
Conversion is currently available from the following objects: - matrix of type integer/numeric - data.frame with integer/numeric data - list of vectors of integer/numeric type
Author(s)
Thibaut Jombart (t.jombart@imperial.ac.uk)
See Also
Related class:
- SNPbin, for storing individual genotypes of
binary SNPs
- genind
Examples
## Not run:
## data to be converted
dat <- list(toto=c(1,1,0,0,2,2,1,2,NA), titi=c(NA,1,1,0,1,1,1,0,0), tata=c(NA,0,3, NA,1,1,1,0,0))
## using the constructor
x1 <- new("genlight", dat)
x1
## using 'as' methods
x2 <- as.genlight(dat)
x3 <- as(dat, "genlight")
identical(x1,x2)
identical(x1,x3)
## End(Not run)