| export {adegenet} | R Documentation |
The function genind2genotype and
genind2hierfstat convert a genind object into,
respectively, a list of genotypes (class genotypes, package
genetics), and a data.frame to be used by the functions of the
package hierfstat.
genind2genotype(x,pop=NULL,res.type=c("matrix","list"))
genind2hierfstat(x,pop=NULL)
x |
a genind object. |
pop |
a factor giving the population of each individual. If NULL, it is seeked in x$pop. If NULL again, all individuals are assumed from the same population. |
res.type |
a character (if a vector, only the first element is retained), indicating the type of result returned. |
The function genind2genotype converts a genind
object into genotypes (package genetics).
If res.type is set to "matrix" (default), the returned value is a
individuals x locus matrix whose columns have the class
genotype. Such data can be used by LDheatmap package to
compute linkage disequilibrium.
If res.type is set to "list", the returned value is a list of
genotypes sorted first by locus and then by population.)
genind2hierfstat returns a data frame where individuals are
in rows. The first columns is a population factor (but stored as
integer); each other column is a locus. Genotypes are coded as
integers (e.g., 44 is an homozygote 4/4, 56 is an heterozygote
5/6).
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
Gregory Warnes and Friedrich Leisch (2007). genetics: Population Genetics. R package version 1.2.1.
Jerome Goudet (2005). HIERFSTAT, a package for R to compute and test
hierarchical F-statistics. Molecular Ecology, 5:184-186
Fstat (version 2.9.3). Software by Jerome
Goudet. http://www2.unil.ch/popgen/softwares/fstat.htm
if(require(hierfstat)){
obj <- read.fstat(system.file("data/diploid.dat",package="hierfstat"))
X <- genind2hierfstat(obj)
X
read.fstat.data(paste(.path.package("hierfstat"),"/data/diploid.dat",sep="",collapse=""),nloc=5)
}
if(require(genetics)){
genind2genotype(obj)
}