FinePop2 (version 0.4)

read.GENEPOP: Create a genotype data object of populations from a GENEPOP format file.

Description

This function reads a GENEPOP format file (Rousset 2008) and parse it into an R data object. This data object provides a summary of genotype/haplotype of each sample, allele frequency in each population, and marker status. This data object is used in downstream analysis of this package.

Usage

read.GENEPOP(genepop, popname = NULL)

Arguments

genepop

A character value specifying the name of the GENEPOP file to be analyzed.

popname

A character value specifying the name of the plain text file containing the names of subpopulations to be analyzed. This text file must not contain other than subpopulation names. The names must be separated by spaces, tabs or line breaks. If this argument is omitted, serial numbers will be assigned as subpopulation names.

Value

num_pop

Number of subpopulations.

pop_sizes

Number of samples in each subpopulation.

pop_names

Names of subpopulations.

ind_names

Names of samples in each subpopulation.

num_loci

Number of loci.

loci_names

Names of loci.

num_allele

Number of alleles at each locus.

allele_list

A list of alleles at each locus.

ind_count

Observed count of genotyped samples in each subpopulation at each locus.

allele_count

Observed count of genotyped alleles in each subpopulation at each locus.

allele_freq

Observed allele frequencies in each subpopulation at each locus.

genotype

Genotypes of each sample at each locus in haploid designation.

call_rate_loci

Call rate of each locus (rate of genotyped samples at each locus).

call_rate_ind

Call rate of each sample (rate of genotyped markers for each sample).

He

Expected heterozigosity in each subpopulation.

Ho

Observed heterozigosity in each subpopulation.

References

Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.

Examples

# NOT RUN {
# Example of GENEPOP file
data(jsmackerel)
jsm.ms.genepop.file <- tempfile()
jsm.popname.file <- tempfile()
cat(jsmackerel$MS.genepop, file=jsm.ms.genepop.file, sep="\n")
cat(jsmackerel$popname, file=jsm.popname.file, sep=" ")

# Read GENEPOP file with subpopulation names.
# Prepare your GENEPOP file and population name file in the working directory.
# Replace "jsm.ms.genepop.file" and "jsm.popname.file" by your file names.
popdata <- read.GENEPOP(genepop=jsm.ms.genepop.file, popname=jsm.popname.file)

# Read GENEPOP file without subpopulation names.
popdata.noname <- read.GENEPOP(genepop=jsm.ms.genepop.file)
# }