adegenet (version 1.4-2)

genpop class: adegenet formal class (S4) for allele counts in populations

Description

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 $.

encoding

UTF-8

Extends

Class "gen", directly. Class "popInfo", directly.

See Also

as.genpop, is.genpop,makefreq, genind, import2genind, read.genetix, read.genepop, read.fstat, na.replace

Examples

obj1 <- import2genind(system.file("files/nancycats.gen",
package="adegenet"))
obj1


obj2 <- genind2genpop(obj1)
obj2

data(microsatt)
# use as.genpop to convert convenient count tab to genpop
obj3 <- as.genpop(microsatt$tab)
obj3

all(obj3@tab==microsatt$tab)
all([e-mail]==rownames(microsatt$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")