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
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
Thibaut Jombart ([email protected])
SNPbin, for storing individual genotypes of
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## 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)
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