adegenet (version 1.2-4)

read.genepop: 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,missing=NA,quiet=FALSE)

Arguments

file

a character string giving the path to the file to convert, with the appropriate extension.

missing

can be NA, 0 or "mean". See details section.

quiet

logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE).

Value

• an object of the class genind

encoding

UTF-8

Details

There are 3 treatments for missing values: - NA: kept as NA. - 0: allelic frequencies are set to 0 on all alleles of the concerned locus. Recommended for a PCA on compositionnal data. - "mean": missing values are replaced by the mean frequency of the corresponding allele, computed on the whole set of individuals. Recommended for a centred PCA.

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