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

In FinePop2: Fine-Scale Population Analysis (Rewrite for Gene-Trait-Environment Interaction Analysis)

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.

Author(s)

Reiichiro Nakamichi

References

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

Examples

# 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)

FinePop2 documentation built on March 26, 2020, 9:01 p.m.