adegenet: genpop – R documentation

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genpop

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).
loc.fac:: locus factor for the columns of tab
loc.n.all:: 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
ploidy:: an integer indicating the degree of ploidy of the genotypes. Beware: 2 is not an integer, but as.integer(2) is.
type:: a character string indicating the type of marker: 'codom' stands for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP).
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 or suppress printing of auxiliary information by specifying verbose = FALSE

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

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


obj2 <- genind2genpop(obj1)
obj2

## Not run: 
data(microsatt)
# use as.genpop to convert convenient count tab to genpop
obj3 <- as.genpop(microsatt$tab)
obj3

all(obj3@tab==microsatt$tab)

# 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")


## End(Not run)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release