read.genepop {adegenet} | R Documentation |
The function read.genepop
reads Genepop data files (.gen) and
convert them into a genind object.
read.genepop(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). |
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
Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population
genetics software for exact tests and ecumenicism. J. Heredity,
86:248-249
import2genind
, df2genind
,
read.fstat
, read.structure
,
read.genetix
obj <- read.genepop(system.file("files/nancycats.gen",package="adegenet")) obj