ade4
package. Moreover, this
package offers methods for manipulating and analyzing information
coming from genetic markers (see below).
=== IMPORTING DATA ===
adegenet
imports data to 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
. Note that df2genind
can be used for any level of ploidy.
=== EXPORTING DATA ===
adegenet
exports data from genind2genotype
- the hierfstat package: see genind2hierfstat
Genotypes can also be recoded from a genind2df
.
=== MANIPULATING DATA ===
Several functions allow one to manipulate genind2genpop
: convert a 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
(makefreq
: returns a table of allelic frequencies from
a repool
merges genoptypes from different
genetic pools into one single 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
- propShared
: computes the proportion of shared
alleles in a set of genotypes (i.e. from a genind object)
- propTyped
: function to investigate missing data in
several ways
- scaleGen
: generic method to scale
adegenetWeb()
.
To cite adegenet, please use the reference given by
citation("adegenet")
(or see reference below).ade4
package for multivariate analysis