adegenet: import2genind – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

import2genind

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).

Usage

import2genind(file, quiet = FALSE, ...)

Arguments

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

Details

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)

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.

Value

an object of the class genind

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

References

Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F. (1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la genetique des populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000, Universite 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

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)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release