adegenet (version 1.4-2)

import: Importing data from several softwares to a genind object

Description

Their are several ways to import genotype data to a genind object: i) from a data.frame with a given format (see df2genind), ii) from a file with a recognized extension, or iii) from an alignement of sequences (see DNAbin2genind). 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 recognized formats are : - GENETIX files (.gtx) - Genepop files (.gen) - Fstat files (.dat) - STRUCTURE files (.str or .stru)

Usage

import2genind(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).

...

other arguments passed to the appropriate 'read' function (currently passed to read.structure)

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. Beware: same data in different formats are not expected to produce 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). Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155: 945-959 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

import2genind, read.genetix, read.fstat, read.structure, read.genepop

Examples

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

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

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

import2genind(system.file("files/nancycats.str",
package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)