genpop {adegenet}R Documentation

adegenet class for allele counts in populations

Description

The objects of class genpop contain alleles counts for several loci.
It consists in a list with several components (see value 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.

Usage

is.genpop(x)
as.genpop(tab = NULL, prevcall = NULL)
## S3 method for class 'genpop':
print(x, ...)
## S3 method for class 'genpop':
summary(object, ...)

Arguments

x an object of class genpop.
tab a populations x alleles matrix of allele counts.
prevcall call of an object, for internal use.
... other -unused- arguments
object an object of class genpop.

Value

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

Author(s)

Thibaut Jombart jombart@biomserv.univ-lyon1.fr

References

See Also

makefreq, genind, import2genind, genetix2genind, genepop2genind, fstat2genind

Examples

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

obj2 <- genind2genpop(obj1)
is.genpop(obj2)
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="replace")
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 1.0-1 Index]