read.genepop: Create a genetic 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. This function is a "lite" version of readGenepop function in diveRsity package (Keenan 2015).

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

References

Keenan K (2015) diveRsity: A Comprehensive, General Purpose Population Genetics Analysis Package. R package version 1.9.89. https://CRAN.R-project.org/package=diveRsity Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.

Examples

Run this code

# data
data(data.JSM)
cat(data.JSM$genepop, file="JSM_genepop.txt", sep="\n")
cat(data.JSM$popname, file="JSM_popname.txt", sep=" ")

# read GENEPOP file with subpopulation names
popdata <- read.genepop(genepop="JSM_genepop.txt", popname="JSM_popname.txt")

# read GENEPOP file without subpopulation names
popdata.noname <- read.genepop(genepop="JSM_genepop.txt")