⚠️There's a newer version (2.1.11) of this package.Take me there.

adegenet (version 1.2-1)

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

Description

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

Copy Link

Version

Install

install.packages('adegenet')

Monthly Downloads

14,047

Version

1.2-1

License

GPL (>=2)

Maintainer

Thibaut Jombart

Last Published

February 7th, 2025

Functions in adegenet (1.2-1)

na.replace-methods

Replace missing values (NA) from an object

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

genind constructor

repool

Pool several genotypes into the same dataset

propTyped-methods

Compute the proportion of typed elements

genpop constructor

export

Conversion functions from adegenet to other R packages

as methods in adegenet

Converting genind/genpop objects to other classes

df2genind

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

Accessors

Accessors for adegenet objects

gstat.randtest

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

Auxiliary functions

Utilities functions for adegenet

read.fstat

Reading data from Fstat

truenames

Restore true labels of an object

hybridize

Simulated hybridization between two samples of populations

microbov

Microsatellites genotypes of 15 cattle breeds

scaleGen-methods

Compute scaled allele frequencies

makefreq

Function to generate allelic frequencies

adegenet-package

The adegenet package

coords.monmonier

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

read.structure

Reading data from STRUCTURE

spcaIllus

Simulated data illustrating the sPCA

nancycats

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

global.rtest

Global and local tests

propShared

Compute proportion of shared alleles

old2new

Convert objects with obsolete classe into new objects

sim2pop

Simulated genotypes of two georeferenced populations

spca

Spatial principal component analysis

fstat

F statistics for genind objects

genind

adegenet formal class (S4) for individual genotypes

read.genetix

Reading data from GENETIX

seploc

Separate data per locus

read.genepop

Reading data from Genepop

monmonier

Boundary detection using Monmonier algorithm

import

Importing data from several softwares to a genind object

dist.genpop

Genetic distances between populations

virtualClasses

Virtual classes for adegenet

chooseCN

Function to choose a connection network

genind2genpop

Conversion from a genind to a genpop object

genpop

adegenet formal class (S4) for allele counts in populations