write.POPDIST: Write Genotypes to a POPDIST File

Description

write.POPDIST uses data from a "genambig" object to write a file formatted for the software POPDIST.

Usage

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

Arguments

object

A "genambig" object. Ploidies and PopInfo are required, and if provided Usatnts may be used to convert alleles to repeat number in order to represent each allele with two digits. Locus names and PopNames are used in the file, but sample names are not.

samples

An optional character vector of samples to use. Must be a subset of Samples(object).

loci

An optional character vector of loci to use. Must be a subset of Loci(object).

file

Character string. File path to which to write.

Value

A file is written but no value is returned.

Details

POPDIST is a program that calculates inter-population distance measures, some of which are available for polyploid samples with allele copy number ambiguity. Each population must be of uniform ploidy, but different populations may have different ploidies.

Two types of warning messages may be printed by write.POPDIST. The first indicates that a population contains individuals of more than one ploidy. In this case a file is still written, but POPDIST may not be able to read it. Separate populations with different ploidies are okay. The second type of warning indicates that an individual has more alleles than its ploidy level. If this occurs, alleles are randomly removed from the genotype that is written to the file.

If necessary, write.POPDIST converts alleles into a two-digit format, similarly to write.Tetrasat. If the value of any allele for a given locus is greater than 99, the function first checks to see if the locus has a Usatnts value greater than 1, and if so divides all alleles by this value and rounds down. If the locus still has alleles with more than two digits, a multiple of 10 is subtracted from all alleles. A zero is placed in front of any allele with one digit.

References

http://gbi.agrsci.dk/~bernt/popgen/

Tomiuk, J., Guldbrandtsen, B. and Loeschcke, B. (2009) Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation. Molecular Ecology Resources 9, 1364-1368.

Guldbrandtsen, B., Tomiuk, J. and Loeschcke, B. (2000) POPDIST version 1.1.1: A program to calculate population genetic distance and identity measures. Journal of Heredity 91, 178--179.

Examples

Run this code

# NOT RUN {
# create a "genambig" object containing the dataset
mygen <- new("genambig", samples=c("a", "b", "c", "d"),
             loci=c("loc1", "loc27"))
mygen <- reformatPloidies(mygen, output="sample")
Description(mygen) <- "Some example data for POPDIST"
PopInfo(mygen) <- c(1,1,2,2)
PopNames(mygen) <- c("Old Orchard Beach", "York Beach")
Ploidies(mygen) <- c(2,2,4,4)
Usatnts(mygen) <- c(2,2)
Genotypes(mygen, loci="loc1") <- list(c(128, 134), c(130),
                                      Missing(mygen), c(126, 128, 132))
Genotypes(mygen, loci="loc27") <- list(c(209,211), c(207,217),
                                       c(207,209,215,221), c(211,223))

# write the file
write.POPDIST(mygen, file="forPOPDIST.txt")

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

# }

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