R: Importing data from several softwares to a genind object
import2genind
R Documentation
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.
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