R: Import Genotype Data from GenoDive File

read.GenoDive {polysat} | 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

### See Also

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

### 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

[Package polysat version 1.7-6 Index]