adegenet (version 1.2-1)

genind2genpop: Conversion from a genind to a genpop object

Description

The function genind2genpop converts genotypes data (genind) into alleles counts per population (genpop).

Usage

genind2genpop(x,pop=NULL,missing=c("NA","0","chi2"),quiet=FALSE)

Arguments

x

an object of class genind.

pop

a factor giving the population of each genotype in 'x'. If note provided, seeked in x@pop, but if given, the argument prevails on x@pop.

missing

can be "NA", "0", or "chi2". See details for more information.

quiet

logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE).

Value

• A genpop object. The component @other in 'x' is passed to the created genpop object.

encoding

UTF-8

Details

The values of the 'missing' argument in genind2genpop have the following effects: - "NA": if all genotypes of a population for a given allele are missing, count value will be NA - "0": if all genotypes of a population for a given allele are missing, count value will be 0 - "chi2": if all genotypes of a population for a given allele are missing, count value will be that of a theoretical count in of a Chi-squared test. This is obtained by the product of the margins sums divided by the total number of alleles.

See Also

genind, genpop, na.replace

Examples

data(nancycats)
  nancycats
  catpop <- genind2genpop(nancycats)
  catpop
  summary(catpop)