| adegenet-package {adegenet} | R Documentation |
This package is devoted to the multivariate analysis of
molecular markers data. It defines two formal (S4) classes:
- genind: a class for data of individuals ("genind" stands for genotypes-individuals).
- genpop: a class for data of groups of individuals ("genpop" stands for genotypes-populations)
For more information about these classes, type "class ? genind" or
"class ? genpop".
Both types of objects store information from molecular markers in a matrix ($tab slot),
that can be directly analyzed using multivariate methods such as
Principal Component Analysis, Correspondance Analysis, etc. See the
"dudi.[...]" methods in the ade4 package. Moreover, this
package offers methods for manipulating and analyzing information
coming from genetic markers (see below).
=== IMPORTING DATA ===
adegenet imports data to genind object from the
following softwares:
- STRUCTURE: see read.structure
- GENETIX: see read.genetix
- FSTAT: see read.fstat
- Genepop: see read.genepop
To import data from any of these formats, you can also use the general
function import2genind.
It is also possible to read genotypes coded by character strings from
a data.frame in which genotypes are in rows, markers in columns. For
this, use df2genind.
=== EXPORTING DATA ===
adegenet exports data from genind object to
formats recognized by other R packages:
- the genetics package: see genind2genotype
- the hierfstat package: see genind2hierfstat
Genotypes can also be recoded from a genind object into
a data.frame of character strings, using any separator between
alleles. This covers formats from many softwares like GENETIX or
STRUCTURE. For this, see genind2df.
=== MANIPULATING DATA ===
Several functions allow one to manipulate genind or
genpop objects
- genind2genpop: convert a genind object
to a genpop
- seploc: creates one object per marker
- seppop: creates one object per population
- na.replace: replaces missing data (NA) in an
approriate way
- truenames: restores true names of an object
(genind and genpop use generic labels)
- x[i,j]: create a new object keeping only genotypes (or populations)
indexed by 'i' and the alleles indexed by 'j'.
- makefreq: returns a table of allelic frequencies from
a genpop object.
- repool merges genoptypes from different
genetic pools into one single genind object.
=== ANALYZING DATA ===
Several functions allow to use usual, and less usual analyses:
- HWE.test.genind: performs HWE test for all
populations and loci combinations
- gstat.randtest: performs a Monte Carlo test of Goudet's G statistic, measuring
population structure (based on g.stat.glob package hierfstat).
- dist.genpop: computes 5 genetic distances among populations.
- monmonier: implementation of the Monmonier algorithm,
used to seek genetic boundaries among individuals or populations. Optimized boundaries can be obtained using
optimize.monmonier. Object of the class
monmonier can be plotted and printed using the corresponding
methods.
- hybridize: implements hybridization between two populations.
- spca: implements Jombart et al. (in revision) spatial
Principal Component Analysis
- global.rtest: implements Jombart et al. (2008)
test for global spatial structures
- local.rtest: implements Jombart et al. (2008)
test for local spatial structures
Adegenet also proposes several real or simulated datasets.
For more information, visit the adegenet website by typing
adegenetWeb().
To cite adegenet, please use the reference given by
citation("adegenet") (or see reference below).
| Package: | adegenet |
| Type: | Package |
| Version: | 1.1-1 |
| Date: | 2008-04-18 |
| License: | GPL (>=2) |
Thibaut Jombart <jombart@biomserv.univ-lyon1.fr>
with contributions of Peter Solymos
Jombart T. (2008) adegenet: a R package for the multivariate analysis of genetic markers
Bioinformatics. doi: 10.1093/bioinformatics/btn129
See adegenet website: http://adegenet.r-forge.r-project.org/
Please post your questions on 'the adegenet forum': adegenet-forum@lists.r-forge.r-project.org
The ade4 package for multivariate analysis