write.GenoDive: Write a File in GenoDive Format

In polysat: Tools for Polyploid Microsatellite Analysis

Write a File in GenoDive Format

Description

write.GenoDive uses data from a genambig object to create a file formatted for the software GenoDive.

Usage

write.GenoDive(object, digits = 2, file = "",
               samples = Samples(object), loci = Loci(object))

Arguments

object	A genambig object containing genotypes, ploidies, population identities, microsatellite repeat lengths, and description for the dataset of interest.
digits	An integer indicating how many digits to use to represent each allele (usually 2 or 3).
file	A character string of the file path to which to write.
samples	A character vector of samples to include in the file. A subset of Samples(object).
loci	A character vector of loci to include in the file. A subset of Loci(object).

Details

The number of individuals, number of populations, number of loci, and maximum ploidy of the sample are calculated automatically and entered in the second line of the file. If the maximum ploidy needs to be reduced by random removal of alleles, it is possible to do this in the software GenoDive after importing the data. The genambig object should not have individuals with more alleles than the highest ploidy level listed in its Ploidies slot.

Several steps happen in order to convert alleles to the right format. First, all instances of the missing data symbol are replaced with zero. Alleles are then divided by the numbers provided in Usatnts(object) (and rounded down if necessary) in order to convert them from nucleotides to repeat numbers. If the alleles are still too big to be represented by the number of digits specified, write.GenoDive repeatedly subtracts a number (10^(digits-1); 10 if digits=2) from all alleles at a locus until the alleles are small enough. Alleles are then converted to characters, and a leading zero is added to an allele if it does not have enough digits. These alleles are concatenated at each locus so that each sample*locus genotype is an uninterrupted string of numbers.

Value

A file is written but no value is returned.

Author(s)

Lindsay V. Clark

References

Meirmans, P. G. and Van Tienderen P. H. (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes 4, 792-794.

http://www.bentleydrummer.nl/software/software/GenoDive.html

See Also

read.GenoDive, write.Structure, write.ATetra, write.Tetrasat, write.GeneMapper, write.POPDIST, write.SPAGeDi

Examples

# set up the genotype object (usually done by reading a file)
mysamples <- c("Mal", "Inara", "Kaylee", "Simon", "River", "Zoe",
               "Wash", "Jayne", "Book")
myloci <- c("loc1", "loc2")
mygendata <- new("genambig", samples=mysamples, loci=myloci)
mygendata <- reformatPloidies(mygendata, output="sample")
Genotypes(mygendata, loci="loc1") <- list(c(304,306), c(302,310),
                                          c(306), c(312,314),
    c(312,314), c(308,310), c(312), c(302,308,310), c(-9))
Genotypes(mygendata, loci="loc2") <- list(c(118,133), c(121,130),
                                          c(122,139), c(124,133),
    c(118,124), c(121,127), c(124,136), c(124,127,136), c(121,130))
Usatnts(mygendata) <- c(2,3)
PopNames(mygendata) <- c("Core","Outer Rim")
PopInfo(mygendata) <- c(2,1,2,1,1,2,2,2,1)
Ploidies(mygendata) <- c(2,2,2,2,2,2,2,3,2)
Description(mygendata) <- "Serenity crew"

## Not run: 
# write files (use file="" to write to the console instead)
write.GenoDive(mygendata, digits=2, file="testGenoDive2.txt")
write.GenoDive(mygendata, digits=3, file="testGenoDive3.txt")

## End(Not run)

polysat documentation built on Aug. 23, 2022, 5:07 p.m.