read.genepop: Reading data from Genepop

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Reading data from Genepop

Description

The function read.genepop reads Genepop data files (.gen) and convert them into a genind object.

Usage

read.genepop(file, ncode = 2L, quiet = FALSE)

Arguments

file	a character string giving the path to the file to convert, with the appropriate extension.
ncode	an integer indicating the number of characters used to code an allele.
quiet	logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE).

Details

Note: read.genepop is meant for DIPLOID DATA ONLY. Haploid data with the Genepop format can be read into R using read.table or read.csv after removing headers and 'POP' lines, and then converted using df2genind.

Value

an object of the class genind

Author(s)

Thibaut Jombart [e-mail]

References

Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249

See Also

import2genind, df2genind, read.fstat, read.structure, read.genetix

Examples

obj <- read.genepop(system.file("files/nancycats.gen",package="adegenet"))
obj

adegenet documentation built on Feb. 16, 2023, 6 p.m.