as.genlight: Conversion to class "genlight"

In adegenet: Exploratory Analysis of Genetic and Genomic Data

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 ([e-mail])

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)

adegenet documentation built on Feb. 16, 2023, 6 p.m.