import {adegenet} | R Documentation |
Their are two ways to import genotyping data to a genind object: from
a data.frame with a given format (see df2genind
, or from a file with a
recognized extension.
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)
import2genind(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). |
... |
other arguments passed to the appropriate 'read' function
(currently passed to read.structure ) |
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.
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).
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
import2genind
, read.genetix
,
read.fstat
, read.structure
, read.genepop
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"), n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)