read.GenoDive: Import Genotype Data from GenoDive File
In polysat: Tools for Polyploid Microsatellite Analysis

read.GenoDive

R Documentation

Import Genotype Data from GenoDive File

Description

read.GenoDive takes a text file in the format for the software GenoDive and produces a genambig object.

Usage

read.GenoDive(infile)

Arguments

infile

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

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, which is written to the Description slot of the genambig object. 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 written to the PopNames slot of the genambig object. 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 locus 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(object) (the default, -9) is written in that genotype slot in the genambig object. 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.

Value

A genambig object containing the data from the file.

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

Examples

# create data file (normally done in a text editor or spreadsheet software)
myfile <- tempfile()
cat(c("example comment line", "5\t2\t2\t3\t2", "pop1", "pop2",
      "pop\tind\tloc1\tloc2", "1\tJohn\t102\t1214",
      "1\tPaul\t202\t0", "2\tGeorge\t101\t121213",
      "2\tRingo\t10304\t131414","1\tYoko\t10303\t120014"),
    file = myfile, sep = "\n")

# import file data
exampledata <- read.GenoDive(myfile)

# view data
summary(exampledata)
viewGenotypes(exampledata)
exampledata

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