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 $.
tab
:loc.names
:loc.fac
:tab
loc.nall
:all.names
:call
:ind.names
:ind.names
.ploidy
:pop
:pop.names
:other
:
Class "gen"
, directly.
Class "indInfo"
, directly.
signature(x = "genind")
: give the names of the
components of a genind objectsignature(x = "genind")
: prints a genind objectsignature(object = "genind")
: shows a genind
object (same as print)signature(object = "genind")
: summarizes a
genind object, invisibly returning its contentsignature(object = "genind")
: returns the number
of loci of the object
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
as.genind
, is.genind
, genind2genpop
,
genpop
, import2genind
,
read.genetix
, read.genepop
,
read.fstat
, na.replace
showClass("genind") obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"),missing="mean") obj validObject(obj) summary(obj) # test inter-colonies structuration if(require(hierfstat)){ gtest <- gstat.randtest(obj,nsim=99) gtest plot(gtest) } # perform an inter-class PCA if(require(ade4)){ pca1 <- dudi.pca(obj@tab,scannf=FALSE,scale=FALSE) pcabet1 <- between(pca1,obj@pop,scannf=FALSE) pcabet1 s.class(pcabet1$ls,obj@pop,sub="Inter-class PCA",possub="topleft",csub=2) add.scatter.eig(pcabet1$eig,2,xax=1,yax=2) }