# Write Genotype Data in Tetrasat Format Given a `genambig` object, `write.Tetrasat` creates a file that can be read by the software Tetrasat and Tetra. ```r 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. ## Returns A file is written but no value is returned. ## 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. ## Author(s) Lindsay V. Clark ## See Also `read.Tetrasat`, `write.GeneMapper`, `write.ATetra`, `write.POPDIST` ## Examples ```r # 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) ```

write.Tetrasat function