read.genetix {adegenet} | R Documentation |
The function read.genetix
reads GENETIX data files (.gtx) and
convert them into a genind object.
read.genetix(file=NULL,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). |
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.
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 genetique des
populations. Laboratoire Genome, Populations, Interactions, CNRS UMR
5000, Université de Montpellier II, Montpellier (France).
import2genind
, df2genind
,
read.fstat
, read.structure
, read.genepop
obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet")) obj