export: Conversion functions from adegenet to other R packages

Description

The function genind2genotype and genind2hierfstat convert a genind object into, respectively, a list of genotypes (class genotypes, package genetics), and a data.frame to be used by the functions of the package hierfstat.

Usage

genind2genotype(x,pop=NULL,res.type=c("matrix","list"))
genind2hierfstat(x,pop=NULL)

Arguments

a genind object.

pop

a factor giving the population of each individual. If NULL, it is seeked in x$pop. If NULL again, all individuals are assumed from the same population.

res.type

a character (if a vector, only the first element is retained), indicating the type of result returned.

Value

The function genind2genotype converts a genind object into genotypes (package genetics). If res.type is set to "matrix" (default), the returned value is a individuals x locus matrix whose columns have the class genotype. Such data can be used by LDheatmap package to compute linkage disequilibrium. If res.type is set to "list", the returned value is a list of genotypes sorted first by locus and then by population.) genind2hierfstat returns a data frame where individuals are in rows. The first columns is a population factor (but stored as integer); each other column is a locus. Genotypes are coded as integers (e.g., 44 is an homozygote 4/4, 56 is an heterozygote 5/6).

encoding

UTF-8

References

Gregory Warnes and Friedrich Leisch (2007). genetics: Population Genetics. R package version 1.2.1.