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adegenet

adegenet: a R Package for the Multivariate Analysis of Genetic Markers

This wiki is dedicated to the development of adegenet. It is relevant for developers of the package, developers of other packages depending on adegenet, and for users who want to be using the latest features as well.

The adegenet website is available at http://adegenet.r-forge.r-project.org/.

The following sections are available:

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Version

Install

install.packages('adegenet')

Monthly Downloads

14,047

Version

2.0.1

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

February 15th, 2016

Functions in adegenet (2.0.1)

adegenet formal class (S4) for individual genotypes

Auxiliary functions

Auxiliary functions for adegenet

Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)

Simulation of genealogies of haplotypes

Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)

Discriminant Analysis of Principal Components (DAPC)

Compute minor allele frequency

Test differences in expected heterozygosity (Hs)

Conversion from a genind to a genpop object

Inbreeding estimation

Likelihood-based estimation of inbreeding

Plotting genlight objects

Extended HGDP-CEPH dataset

Convert a data.frame of allele data to a genind object.

Simulation of simple genlight objects

Convert a genind object to a data.frame.

adegenet formal class (S4) for allele counts in populations

Access and manipulate the population hierarchy for genind or genlight objects.

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

Read large DNA alignments into R

Boundary detection using Monmonier algorithm

Reading Single Nucleotide Polymorphism data

adegenet.package

The adegenet package

Manipulate the population factor of genind objects.

Identify mutations between DNA sequences

Pairwise distance plots

Principal Component Analysis for genlight objects

Represents a cloud of points with colors

Function to choose a connection network

Formal class "genlight"

Importing data from several softwares to a genind object

Formal class "SNPbin"

propTyped-methods

Compute the proportion of typed elements

Simulated data illustrating the sPCA

Compute proportion of shared alleles

Convert objects with obsolete classes into new objects

Access allele counts or frequencies

Adegenet servers

Web servers for adegenet

as methods in adegenet

Converting genind/genpop objects to other classes

Select genotypes of well-represented populations

Seasonal influenza (H3N2) HA segment data

Conversion to class "genlight"

initialize,genind-method

genind constructor

Assess polymorphism in genind/genpop objects

Reading data from STRUCTURE

Represents a cloud of points with colors

Compute allelic frequencies

extract.PLINKmap

Reading PLINK Single Nucleotide Polymorphism data

Analyse the position of polymorphic sites

Restore true labels of an object

Pool several genotypes into a single dataset

Simulated genotypes of two georeferenced populations

Microsatellites genotypes of 15 cattle breeds

initialize,genpop-method

genpop constructor

Function hybridize takes two genind in inputs and generates hybrids individuals having one parent in both objects.

Separate data per locus

genlight auxiliary functions

Auxiliary functions for genlight objects

Global and local tests

Access and manipulate the population strata for genind or genlight objects.

Reading data from Fstat

Genetic distances between populations

SequencesToGenind

Importing data from an alignement of sequences to a genind object

Virtual classes for adegenet

Spatial principal component analysis

Simulated data illustrating the DAPC

find.cluster: cluster identification using successive K-means

Reading data from GENETIX

SeqTrack algorithm for reconstructing genealogies

Conversion to class "SNPbin"

Accessors for adegenet objects

Functions to access online resources for adegenet

Expected heterozygosity (Hs)

Graphics for Discriminant Analysis of Principal Components (DAPC)

Reading data from Genepop

coords.monmonier

Returns original points in results paths of an object of class 'monmonier'

DAPC cross-validation

Cross-validation for Discriminant Analysis of Principal Components (DAPC)

Genetic transitive graphs

Extract Single Nucleotide Polymorphism (SNPs) from alignments

Compute scaled allele frequencies

Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France)

Separate genotypes per population