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adegenet (version 1.1-1)

adegenet: a R package for the multivariate analysis of genetic markers.

Description

Classes and functions for genetic data analysis within the multivariate framework.

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Version

Install

install.packages('adegenet')

Monthly Downloads

11,337

Version

1.1-1

License

GPL (>=2)

Maintainer

Thibaut Jombart

Last Published

February 7th, 2025

Functions in adegenet (1.1-1)

gstat.randtest

Goudet's G-statistic Monte Carlo test for genind object

genind constructor

fstat

F statistics for genind objects

adegenet-package

The adegenet package

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

dist.genpop

Genetic distances between populations

df2genind

Convert a data.frame of genotypes to a genind object, and conversely.

genind

adegenet formal class (S4) for individual genotypes

genpop constructor

virtualClasses

Virtual classes for adegenet

chooseCN

Function to choose a connection network

Accessors

Accessors for adegenet objects

repool

Pool several genotypes into the same dataset

spcaIllus

Simulated data illustrating the sPCA

coords.monmonier

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

nancycats

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

genpop

adegenet formal class (S4) for allele counts in populations

read.genepop

Reading data from Genepop

hybridize

Simulated hybridization between two samples of populations

microbov

Microsatellites genotypes of 15 cattle breeds

global.rtest

Global and local tests

makefreq

Function to generate allelic frequencies

genind2genpop

Conversion from a genind to a genpop object

seploc

Separate data per locus

read.genetix

Reading data from GENETIX

read.structure

Reading data from STRUCTURE

monmonier

Boundary detection using Monmonier algorithm

spca

Spatial principal component analysis

export

Conversion functions from adegenet to other R packages

old2new

Convert objects with obsolete classe into new objects

read.fstat

Reading data from Fstat

truenames

Restore true labels of an object

na.replace-methods

Replace missing values (NA) from an object

sim2pop

Simulated genotypes of two georeferenced populations

import

Importing data from several softwares to a genind object

Auxiliary functions

Utilities functions for adegenet