adegenet (version 1.0-0)

import: Conversion function for adegenet

Description

The function import2genind detects the extension of the file given in argument and seeks for an appropriate import function to create a genind object. Current functions are : - genetix2genind for GENETIX files (.gtx). Note that this function is called by the others. - genepop2genind for Genepop files (.gen) - fstat2genind for Fstat files .dat

Usage

import2genind(file,missing=NA,quiet=FALSE)
genetix2genind(file=NULL,X=NULL,pop=NULL,missing=NA,quiet=FALSE)
genepop2genind(file,missing=NA,quiet=FALSE)
fstat2genind(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).

X

if file is not provided, genetix2genind can be used on a data frame with genotypes in GENETIX format (e.g. "080082" for an heterozygote with alleles 80 and 82); individuals are in rows, loci are in columns. Missing values are coded as "

pop

an optional factor giving the population of each genotype in 'x'.

Value

• an object of the class genind

Details

There are 3 treatments for missing values: - NA: kept as NA.  - 0: missing values are considered as zero. Recommended for a PCA on compositionnal data.  - "mean": missing values are given the mean frequency of the corresponding allele. Recommended for a centred PCA. Beware: same data in different formats are not expected to produce the exactly the same genind objects. For instance, conversions made by GENETIX to Fstat may change the the sorting of the genotypes; GENETIX stores individual names whereas Fstat does not; Genepop chooses a sample's name from the name of its last genotype; etc.

References

Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F. (1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier (France). Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249 Fstat (version 2.9.3). Software by Jerome Goudet. http://www2.unil.ch/popgen/softwares/fstat.htm Excoffier L. & Heckel G.(2006) Computer programs for population genetics data analysis: a survival guide Nature, 7: 745-758

See Also

read.fstat.data

Examples

genetix2genind(system.file("files/nancycats.gtx",package="adegenet"))

fstat2genind(system.file("files/nancycats.dat",package="adegenet"))

genepop2genind(system.file("files/nancycats.gen",package="adegenet"))

import2genind(system.file("files/nancycats.gtx",
package="adegenet"))

if(require(hierfstat)){
obj <- fstat2genind(system.file("data/diploid.dat",package="hierfstat"))
obj
}