ade4
package. However, this package also provides interfaces with other
packages, making Hardy-Weinberg equilibrium test, F statistics,
Goudet's G test for population structure, or linkage disequilibrium
measure available directly or using simple conversion functions.
The basic class of object is genind, and contains
genotypes (genind stands for genotypes-individuals).
It can be obtained by converting files from GENETIX, Fstat
and Genepop using import2genind.
The second class is genpop: such object contains alleles counts per populations and
loci. It can be obtained from any genind object using
genind2genpop.
It is also possible to obtain a table of allelic frequencies using
makefreq on a genpop object.
In all cases, missing data can be treated using different options.
The package proposes useful functions for genind objects:
- HWE.test.genind to test for Hardy-Weinberg equilibrium on every locus
x population combinaisons (based on HWE.test, package
genetics).
- gstat.randtest is Monte Carlo test (class
randtest) of Goudet's G statistic measuring
population structure (based on g.stat.glob, package
hierfstat).
- genind2genotype assures conversion into
genotype objects used in genetics
and LDheatmap packages.
- genind2hierfstat assures conversion into
the format (particular data.frame) used in hierfstat package.
Lastly, several genetic distances between populations can be computed
using dist.genpop.
Genetic distances between individuals are not yet implemented. These are the essential functions provided by the package:
genind: adegenet class for individual genotypes
genpop: adegenet class for allele counts in
populations
import2genind: Conversion function for adegenet (from
GENETIX, Fstat, Genepop)
makefreq: Function to generate allelic frequencies
HWE.test.genind: Hardy-Weinberg Equilibrium test for
multilocus data
gstat.randtest: Monte Carlo test of Goudet's G statistic
for multilocus data
ade4 package for multivariate analysis