| genind {adegenet} | R Documentation |
The S4 class genind is used to store individual genotypes.
It contains several components described in the 'slots' section).
The summary of a genind object invisibly returns a list of component.
The function .valid.genind is for internal use.
The function genind creates an empty valid genind object.
Note that as in other S4 classes, slots are accessed using @ instead
of $.
tab:loc.names:loc.fac:tabloc.nall:all.names:call:ind.names:ind.names.pop:pop.names:other:
Class "gen", directly.
Class "indInfo", directly.
signature(x = "genind"): give the names of the
components of a genind objectsignature(x = "genind"): prints a genind objectsignature(object = "genind"): shows a genind
object (same as print)signature(object = "genind"): summarizes a
genind object, invisibly returning its contentThibaut Jombart jombart@biomserv.univ-lyon1.fr
as.genind, is.genind, genind2genpop,
genpop, import2genind,
read.genetix, read.genepop,
read.fstat, na.replace
showClass("genind")
obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"),missing="mean")
obj
validObject(obj)
summary(obj)
# test inter-colonies structuration
if(require(hierfstat)){
gtest <- gstat.randtest(obj,nsim=99)
gtest
plot(gtest)
}
# perform an inter-class PCA
if(require(ade4)){
pca1 <- dudi.pca(obj@tab,scannf=FALSE,scale=FALSE)
pcabet1 <- between(pca1,obj@pop,scannf=FALSE)
pcabet1
s.class(pcabet1$ls,obj@pop,sub="Inter-class PCA",possub="topleft",csub=2)
add.scatter.eig(pcabet1$eig,2,xax=1,yax=2)
}