polysat (version 1.7-7)

write.Tetrasat: 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 = "")

Value

A file is written but no value is returned.

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.

Author

Lindsay V. Clark

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.

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

if (FALSE) {
# write a Tetrasat file
write.Tetrasat(mygendata, file="tetrasattest.txt")

# view the file
cat(readLines("tetrasattest.txt"),sep="\n")
}
# \dontshow{
write.Tetrasat(mygendata, file=tempfile())
# }