adegenet-package {adegenet} | R Documentation |
This package is devoted to manipulate data obtained from
molecular markers. The newly defined classes of object facilitate their
analysis within the multivariate framework of the 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.
Since the second version (1.0-1), adegenet
also includes
spatial analysis function like Monmonier algorithm (see
monmonier
) to define genetic boundaries among
individuals or populations.
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.
Moreover, several genetic distances between populations can be computed
using dist.genpop
.
Genetic distances between individuals are not yet implemented.
Lastly, the Monmonier algorithm is implemented to seek genetic
boundaries. The main function is monmonier
, but
better (optimized) boundaries can be obtained using
optimize.monmonier
. Object of the class monmonier
can be plotted and printed using the corresponding methods.
Package: | adegenet |
Type: | Package |
Version: | 1.0-2 |
Date: | 2007-09-08 |
License: | GPL version 2 or newer |
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
monmonier
: Monmonier algorithm to find genetic
boundaries among genetic entities on a connection network
Thibaut Jombart <jombart@biomserv.univ-lyon1.fr>
See adegenet website: http://pbil.univ-lyon1.fr/software/adegenet/
ade4
package for multivariate analysis