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

genpop class {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).

`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

### See Also

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

### 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)

[Package adegenet version 2.1.4 Index]