genpop {adegenet}R Documentation

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 $.

Slots

tab:
matrix of alleles counts for each combinaison of population -in rows- and alleles -in columns-. Rows and columns are given generic names.
loc.names:
character vector containing the real names of the loci
loc.fac:
locus factor for the columns of tab
loc.nall:
integer vector giving the number of alleles per locus
all.names:
list having one component per locus, each containing a character vector of alleles names
call:
the matched call
pop.names:
character vector containing the real names of the populations
other:
(optional) a list containing other information

Extends

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

Methods

names
signature(x = "genpop"): give the names of the components of a genpop object
print
signature(x = "genpop"): prints a genpop object
show
signature(object = "genpop"): shows a genpop object (same as print)
summary
signature(object = "genpop"): summarizes a genpop object, invisibly returning its content
nLoc
signature(object = "genpop"): returns the number of loci of the object

Author(s)

Thibaut Jombart jombart@biomserv.univ-lyon1.fr

See Also

as.genpop, is.genpop,code{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

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")
}

[Package adegenet version 1.2-2 Index]