adegenet (version 2.0.1)

as.genlight: 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

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)