polysat (version 0.1)

write.SPAGeDi: Write Genotypes in SPAGeDi Format

Description

write.SPAGeDi takes a genotype object in the standard polysat format and creates a file that can be read by the software SPAGeDi. The user controls how the genotypes are formatted, and can specify the ploidy, population, and spatial coordinates of each sample.

Usage

write.SPAGeDi(gendata, samples = dimnames(gendata)[[1]],
              loci = dimnames(gendata)[[2]],
              indploidies = rep(4, length(samples)),
              popinfo = rep(1, length(samples)), allelesep = "/",
              digits = 2, file = "",
              spatcoord = data.frame(X = rep(1, length(samples)),
                                     Y = rep(1, length(samples)),
                                     row.names = samples),
              usatnts = rep(2, length(loci)), missing = -9)

Arguments

gendata

A genotype object in the standard polysat format. A two dimensional list of integer vectors, where samples are represented and named in the first dimension, and loci are represented and named in the second dimension. Each vector contains all unique al

samples

Character vector. Samples to write to the file. Must be a subset of dimnames(gendata)[[1]].

loci

Character vector. Loci to write to the file. Must be a subset of dimnames(gendata)[[2]].

indploidies

Integer vector. Ploidy of each sample. This can either be named by sample, or be in the same order as samples.

popinfo

Vector. Population identity (or category) of each individual. This can either be named by sample, or be in the same order as samples.

allelesep

The character that will be used to separate alleles within a genotype. If each allele should instead be a fixed number of digits, with no characters to delimit alleles, set allelesep = "".

digits

Integer. The number of digits used to represent each allele.

file

Character string. The file path to write to.

spatcoord

Data frame. Spatial coordinates of each sample. Column names are used for column names in the file. Row names indicate sample, or if absent it is assumed that the rows are in the same order as samples.

usatnts

Integer vector. Repeat length of each locus (eg. 2 to indicate dinucleotide repeats, or 3 to indicate trinucleotide repeats). If the alleles in gendata are already in repeat lengths rather than nucleotides, the value should be 1. The ve

missing

The symbol used in gendata to indicate missing data.

Value

• A file is written but no value is returned.

Details

popinfo, indploidies, spatcoord, and usatnts can have more samples or loci than are to be written to the file, as long as they are named. The first line of the file contains the number of individuals, number of categories, number of spatial coordinates, number of loci, number of digits for coding alleles, and maximum ploidy, and is generated automatically from the data provided. The function does not write distance intervals to the file, but instead writes 0 to the second line. All alleles for a given locus are divided by the usatnts value for that locus, after all missing data symbols have been replaced with zeros. If necessary, a multiple of 10 is subtracted from all alleles at a locus in order to get the alleles down to the right number of digits. If a genotype has fewer alleles than the indploidies value for that sample, zeros are added up to the ploidy. If the genotype has more alleles than the ploidy, a random subset of alleles is used and a warning is printed. If the genotype has only one allele (is fully heterozygous), then that allele is replicated to the ploidy of the individual. Genotypes are then concatenated into strings, delimited by allelesep. If allelesep="", leading zeros are first added to alleles as necessary to make them the right number of digits.

References

http://ebe.ulb.ac.be/ebe/Software_files/manual_SPAGeDi_1-3.pdf Hardy, O. J. and Vekemans, X. (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618-620.

See Also

read.SPAGeDi, write.GenoDive, write.Structure, write.GeneMapper, write.ATetra, write.Tetrasat, codominant.to.dominant

Examples

# set up data to write (usually read from a file)
mygendata <- array(list(-9), dim=c(4,2),
                   dimnames=list(c("ind1","ind2","ind3","ind4"),
                                 c("loc1", "loc2")))
mygendata["ind1",] <- list(c(102,106,108),c(207,210))
mygendata["ind2",] <- list(c(104),c(204,210))
mygendata["ind3",] <- list(c(100,102,108),c(201,213))
mygendata["ind4",] <- list(c(102,112),c(-9))
myploidies <- c(3,2,2,2)
names(myploidies) <- c("ind1","ind2","ind3","ind4")
myusatnts <- c(2,3)
names(myusatnts) <- c("loc1","loc2")
myspatcoord <- data.frame(X=c(27,29,24,30), Y=c(44,41,45,46),
                          row.names=c("ind1","ind2","ind3","ind4"))

# write a file
write.SPAGeDi(mygendata, indploidies = myploidies, usatnts = myusatnts,
              spatcoord = myspatcoord, file="SpagOutExample.txt")