The function read.genetix reads GENETIX data files (.gtx) and
convert them into a genind object.
Note: read.genetix is meant for DIPLOID DATA ONLY. Haploid
data with the GENETIX format can be read into R using
read.table or read.csv after removing headers and 'POP'
lines, and then converted using df2genind.
Usage
read.genetix(file=NULL,missing=NA,quiet=FALSE)
Arguments
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).
Value
an object of the class genind
encoding
UTF-8
Details
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.
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, Université de Montpellier II, Montpellier (France).