import {adegenet} | R Documentation |
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
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)
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 "000000". |
pop |
an optional factor giving the population of each genotype in 'x'. |
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.
an object of the class genind
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
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
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 }