R: Conversion to class "genlight"

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)

[Package adegenet version 2.1.4 Index]