polysat (version 0.1)

read.GenoDive: Import Genotype Data from GenoDive File

Description

read.GenoDive takes a text file in the format for the software GenoDive and produces a vector indicating which samples are in which populations and a two-dimensional list of vectors containing the genotypes.

Usage

read.GenoDive(infile, missing = -9)

Arguments

infile

A character string. The path to the file to be read.

missing

The symbol used to represent missing data in the output.

Value

• PopData
  A numeric vector containing the population number of each individual. The names of the vector are the names of the individuals.
• Genotypes
  A two-dimensional list of integer vectors, containing genotypes in the same format that is produced and read by other polysat functions. The first dimension is indexed by sample and the second dimension is indexed by locus. Each vector contains all unique alleles for a given sample and locus.

Details

GenoDive is a Mac-only program for population genetic analysis that allows for polyploid data. read.GenoDive imports data from text files formatted for this program. The first line of the file is a comment line, ignored by the function. On the second line, separated by tabs, are the number of individuals, number of populations, number of loci, maximum ploidy (ignored), and number of digits used to code alleles. The following lines contain the names of populations, which are ignored by the function although the number of lines should be the same as the number of populations as specified in the first line. After that is a header line for the genotype data. This line contains, separated by tabs, column headers for populations, clones (optional), and individuals, followed by the name of each locus. The loci names for the genotype object are derived from this line. Each individual is on one line following the genotype header line. Separated by tabs are the population number, the clone number (optional), the individual name (used as the sample name in the output) and the genotypes at each locus. Alleles at one locus are concatenated together in one string without any characters to separate them. Each allele must have the same number of digits, although leading zeros can be omitted. If the only alleles listed for a particular individual and locus are zeros, this is interpreted by read.GenoDive as missing data, and missing (-9 by default) is recorded in the list. GenoDive allows for a genotype to be partially missing but polysat does not; therefore, if an allele is coded as zero but other alleles are recorded for that sample and locus, the output genotype will just contain the alleles that are present, with the zeros thrown out.

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

Examples

# create data file (normally done in a text editor or spreadsheet software)
cat(c("example comment line", "5t2t2t3t2", "pop1", "pop2",
      "poptindtloc1tloc2", "1tJohnt102t1214",
      "1tPault202t0", "2tGeorget101t121213",
      "2tRingot10304t131414","1tYokot10303t120014"),
    file = "genodiveExample.txt", sep = "")

# import file data
exampledata <- read.GenoDive("genodiveExample.txt")

# view data
exampledata$PopData
exampledata$Genotypes[,"loc1"]
exampledata$Genotypes[,"loc2"]