R: Write Genotypes in ATetra Format

write.ATetra {polysat} | R Documentation

## Write Genotypes in ATetra Format

### Description

`write.ATetra` uses genotype and population information contained in a `genambig` object to create a text file of genotypes in the ATetra format.

### Usage

    write.ATetra(object, samples = Samples(object),
                 loci = Loci(object), file = "")

### Arguments

`object` | A `genambig` object containing the dataset of interest. Genotypes, population identities, population names, and the dataset description are used for creating the file. Ploidies must be set to 4.
`samples` | A character vector of samples to write to the file. This is a subset of `Samples(object)`.
`loci` | A character vector of loci to write to the file. This is a subset of `Loci(object)`.
`file` | A character string indicating the path and name to which to write the file.

### Details

Note that missing data are not allowed in ATetra, although `write.ATetra` will still process missing data. When it does so, it leaves all alleles blank in the file for that particular sample and locus, and also prints a warning indicating which sample and locus had missing data.

### Value

A file is written but no value is returned.

### Author(s)

Lindsay V. Clark

### References

http://www.vub.ac.be/APNA/ATetra_Manual-1-1.pdf

van Puyvelde, K., van Geert, A. and Triest, L. (2010) ATETRA, a new software program to analyze tetraploid microsatellite data: comparison with TETRA and TETRASAT. Molecular Ecology Resources 10, 331-334.

### See Also

`read.ATetra`, `write.Tetrasat`, `write.GeneMapper`, `write.POPDIST`

### Examples

    # set up sample data (usually done by reading files)
    mysamples <- c("ind1", "ind2", "ind3", "ind4")
    myloci <- c("loc1", "loc2")
    mygendata <- new("genambig", samples=mysamples, loci=myloci)
    mygendata <- reformatPloidies(mygendata, output="one")
    Genotypes(mygendata, loci="loc1") <- list(c(202,204), c(204),
                                              c(200,206,208,212),
                                              c(198,204,208))
    Genotypes(mygendata, loci="loc2") <- list(c(78,81,84),
                                              c(75,90,93,96,99),
                                              c(87), c(-9))
    PopInfo(mygendata) <- c(1,2,1,2)
    PopNames(mygendata) <- c("this pop", "that pop")
    Ploidies(mygendata) <- 4
    Description(mygendata) <- "Example for write.ATetra."

    ## Not run:
    # write an ATetra file
    write.ATetra(mygendata, file="atetratest.txt")

    # view the file
    cat(readLines("atetratest.txt"),sep="\n")

    ## End(Not run)

[Package polysat version 1.7-6 Index]