R: Write Genotype Data in Tetrasat Format

write.Tetrasat {polysat} | R Documentation

## Write Genotype Data in Tetrasat Format

### Description

Given a `genambig` object, `write.Tetrasat` creates a file that can be read by the software Tetrasat and Tetra.

### Usage

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

### Arguments

`object` | A `genambig` object containing the dataset of interest. Genotypes, population identities, microsatellite repeat lengths, and the dataset description of `object` are used by the function.
`samples` | A character vector of samples to write to the file. Should be a subset of `Samples(object)`.
`loci` | A character vector of loci to write to the file. Should be a subset of `Loci(object)`.
`file` | A character string indicating the file to which to write.

### Details

Tetrasat files are space-delimited text files in which all alleles at a locus are concatenated into a string eight characters long. Population names or numbers are not used in the file, but samples are ordered by population, with the line “Pop” delimiting populations.

`write.Tetrasat` divides each allele by the length of the repeat and rounds down in order to convert alleles to repeat numbers. If necessary, it subtracts a multiple of 10 from all alleles at a locus to make all allele values less than 100, or puts a zero in front of the number if it only has one digit. If the individual is fully homozygous at a locus, the single allele is repeated four times. If any genotype has more than four alleles, `write.Tetrasat` picks a random sample of four alleles without replacement, and prints a warning. Missing data are represented by blank spaces.

Sample names should be a maximum of 20 characters long in order for the file to be read correctly by Tetrasat or Tetra.

### Value

A file is written but no value is returned.

### Author(s)

Lindsay V. Clark

### References

Markwith, S. H., Stewart, D. J. and Dyer, J. L. (2006) TETRASAT: a program for the population analysis of allotetraploid microsatellite data. Molecular Ecology Notes 6, 586-589.

Liao, W. J., Zhu, B. R., Zeng, Y. F. and Zhang, D. Y. (2008) TETRA: an improved program for population genetic analysis of allotetraploid microsatellite data. Molecular Ecology Resources 8, 1260–1262.

### See Also

`read.Tetrasat`, `write.GeneMapper`, `write.ATetra`, `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")
    Usatnts(mygendata) <- c(2, 3)
    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)
    Description(mygendata) <- "An example for write.Tetrasat."
    Ploidies(mygendata) <- 4

    ## Not run:
    # write a Tetrasat file
    write.Tetrasat(mygendata, file="tetrasattest.txt")

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

    ## End(Not run)

[Package polysat version 1.7-6 Index]