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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

11,025

Version

2.1.10

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/thibautjombart/adegenet

Maintainer

Zhian N. Kamvar

Last Published

January 26th, 2023

Functions in adegenet (2.1.10)

Compute Akaike Information Criterion (AIC) for snapclust

Expected heterozygosity (Hs)

Compute Akaike Information Criterion for small samples (AICc) for snapclust

Compute Bayesian Information Criterion (BIC) for snapclust

Compute Akaike Information Criterion for small samples (AICc) for snapclust

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

Accessors for adegenet objects

Test differences in expected heterozygosity (Hs)

Seasonal influenza (H3N2) HA segment data

Formal class "SNPbin"

Genotype composition plot

Function to choose a connection network

Conversion to class "SNPbin"

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

Auxiliary functions

Auxiliary functions for adegenet

coords.monmonier

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

Represents a cloud of points with colors

Conversion to class "genlight"

as methods in adegenet

Converting genind/genpop objects to other classes

adegenet.package

The adegenet package

Genetic distances between populations

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

Simulated data illustrating the DAPC

.internal_C_routines

Internal C routines

Read large DNA alignments into R

Extended HGDP-CEPH dataset

Discriminant Analysis of Principal Components (DAPC)

Graphics for Discriminant Analysis of Principal Components (DAPC)

export_to_mvmapper

Export analysis for mvmapper visualisation

Extract Single Nucleotide Polymorphism (SNPs) from alignments

adegenet formal class (S4) for individual genotypes

Formal class "genlight"

adegenet formal class (S4) for allele counts in populations

Genetic transitive graphs

genlight auxiliary functions

Auxiliary functions for genlight objects

Plotting genlight objects

Principal Component Analysis for genlight objects

Conversion from a genind to a genpop object

find.cluster: cluster identification using successive K-means

Convert a genind object to a data.frame.

Represents a cloud of points with colors

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

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

Toy hybrid dataset

Importing data from several softwares to a genind object

Simulation of simple genlight objects

Compute allelic frequencies

Inbreeding estimation

Likelihood-based estimation of inbreeding

Assess polymorphism in genind/genpop objects

Simulation of genealogies of haplotypes

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

Identify mutations between DNA sequences

Pairwise distance plots

initialize,genind-method

genind constructor

Manipulate the population factor of genind objects.

Boundary detection using Monmonier algorithm

Microsatellites genotypes of 15 cattle breeds

Compute minor allele frequency

initialize,genpop-method

genpop constructor

Convert objects with obsolete classes into new objects

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

Pool several genotypes into a single dataset

Reading Single Nucleotide Polymorphism data

Reading data from STRUCTURE

Reading data from Genepop

extract.PLINKmap

Reading PLINK Single Nucleotide Polymorphism data

Reading data from GENETIX

Compute proportion of shared alleles

Reading data from Fstat

Adegenet servers

Web servers for adegenet

SeqTrack algorithm for reconstructing genealogies

propTyped-methods

Compute the proportion of typed elements

Maximum-likelihood genetic clustering using EM algorithm

SequencesToGenind

Importing data from an alignement of sequences to a genind object

Simulated genotypes of two georeferenced populations

Select genotypes of well-represented populations

Separate data per locus

When you need a break...

Compute scaled allele frequencies

Separate genotypes per population

Microsatellites genotypes of 781 swallowtail butterflies from 40 populations in Alberta and British Columbia, Canada

Analyse the position of polymorphic sites

Monte Carlo test for sPCA

snapclust.choose.k

Choose the number of clusters for snapclust using AIC, BIC or AICc

Identification of structural SNPs

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

Spatial principal component analysis

DAPC cross-validation

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

Functions to access online resources for adegenet

Access allele counts or frequencies

Virtual classes for adegenet

Restore true labels of an object

Global and local tests

Simulated data illustrating the sPCA