R: Convert Data to genind Format

gendata.to.genind {polysat} | R Documentation

## Convert Data to genind Format

### Description

This is a function for exporting data to the package adegenet.

### Usage

    gendata.to.genind(object, samples = Samples(object), loci = Loci(object))

### Arguments

`object` | A `"genambig"` or (preferably) a `"genbinary"` object.
`samples` | A character vector indicating the samples to include in the output.
`loci` | A character vector indicating the loci to include in the output.

### Details

`gendata.to.genind` converts a `"genambig"` or `"genbinary"` object to a `"genind"` object using the package adegenet. Each individual must have a single ploidy. Ploidy and population information are carried over to the new object. Data will be coded as presence/absence in the new object. The locus names in the new object are locus and allele names seperated by a hyphen.

adegenet must be installed in order to use this function.

### Value

A genetic dataset in the `"genind"` class, ready for use in adegenet.

### Author(s)

Lindsay V. Clark

### References

http://adegenet.r-forge.r-project.org/

Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405.

### See Also

`freq.to.genpop`

### Examples

    # create a "genambig" object
    mydata <- new("genambig", samples=c("a","b","c","d"), loci=c("e","f"))
    PopNames(mydata) <- c("G","H")
    PopInfo(mydata) <- c(1,1,2,2)
    mydata <- reformatPloidies(mydata, output="one")
    Ploidies(mydata) <- 3
    Genotypes(mydata, loci="e") <- list(c(100),c(100,102),
                                        c(98,102,104),c(102,106))
    Genotypes(mydata, loci="f") <- list(c(200,202,204),Missing(mydata),
                                        c(210,212),c(204,210,214))

    # convert to "genind"; not tested as it takes several seconds to load adegenet

    if(require("adegenet")){
      mydata2 <- gendata.to.genind(mydata)
      mydata2@tab
      locNames(mydata2)
      indNames(mydata2)
      popNames(mydata2)
      pop(mydata2)
    }

[Package polysat version 1.7-6 Index]