| genpop {adegenet} | R Documentation |
An object of class genpop contain alleles counts
for several loci.
It contains several components (see 'slots' section).
Such object is obtained using genind2genpop which converts
individuals genotypes of known population into a genpop object.
Note that the function summary of a genpop object
returns a list of components.
Note that as in other S4 classes, slots are accessed using @ instead
of $.
tab:loc.names:loc.fac:tabloc.nall:all.names:call:pop.names:other:
Class "gen", directly.
Class "popInfo", directly.
signature(x = "genpop", method = "ANY", diag = "ANY", upper = "ANY", p = "missing"): ... signature(x = "genpop"): ... signature(object = "genpop"): ... signature(object = "genpop"): ... Thibaut Jombart jombart@biomserv.univ-lyon1.fr
as.genpop, is.genpop,code{makefreq}, genind, import2genind, read.genetix, read.genepop, read.fstat, na.replace
obj1 <- import2genind(system.file("files/nancycats.gen",
package="adegenet"))
obj1
obj2 <- genind2genpop(obj1)
obj2
if(require(ade4)){
data(microsatt)
# use as.genpop to convert convenient count tab to genpop
obj3 <- as.genpop(microsatt$tab)
obj3
all(obj3@tab==microsatt$tab)
all(obj3@pop.names==rownames(microsatt$tab))
# it worked
# perform a correspondance analysis
obj4 <- genind2genpop(obj1,missing="chi2")
ca1 <- dudi.coa(as.data.frame(obj4@tab),scannf=FALSE)
s.label(ca1$li,sub="Correspondance Analysis",csub=2)
add.scatter.eig(ca1$eig,2,xax=1,yax=2,posi="top")
}