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adegenet (version 1.2-4)

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

14,047

Version

1.2-4

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

April 16th, 2010

Functions in adegenet (1.2-4)

df2genind

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

Simulation of populations of haplotypes
genpop constructor

genpop constructor
seploc

Separate data per locus
H3N2

Seasonal influenza (H3N2) HA segment data
dist.genpop

Genetic distances between populations
genind constructor

genind constructor
read.genepop

Reading data from Genepop
HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data
as methods in adegenet

Converting genind/genpop objects to other classes
coords.monmonier

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

Utilities functions for adegenet
microbov

Microsatellites genotypes of 15 cattle breeds
genind class

adegenet formal class (S4) for individual genotypes
fstat

F statistics for genind objects
virtualClasses

Virtual classes for adegenet
sim2pop

Simulated genotypes of two georeferenced populations
genpop class

adegenet formal class (S4) for allele counts in populations
scaleGen-methods

Compute scaled allele frequencies
haploGen

Simulation of populations of haplotypes
read.structure

Reading data from STRUCTURE
adegenet-package

The adegenet package
seppop

Separate genotypes per population
truenames

Restore true labels of an object
eHGDP

Extended HGDP-CEPH dataset
nancycats

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

Function to choose a connection network
na.replace-methods

Replace missing values (NA) from an object
spcaIllus

Simulated data illustrating the sPCA
import

Importing data from several softwares to a genind object
spca

Spatial principal component analysis
loadingplot

Represents a cloud of points with colors
old2new

Convert objects with obsolete classe into new objects
propShared

Compute proportion of shared alleles
colorplot

Represents a cloud of points with colors
isPoly-methods

Assess polymorphism in genind/genpop objects
find.clusters

find.cluster: cluster identification using successive K-means
seqTrack

SeqTrack algorithm
gstat.randtest

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

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

Global and local tests
propTyped-methods

Compute the proportion of typed elements
dapcIllus

Simulated data illustrating the DAPC
genind2genpop

Conversion from a genind to a genpop object
monmonier

Boundary detection using Monmonier algorithm
Hs

Expected heterozygosity
repool

Pool several genotypes into a single dataset
hybridize

Simulated hybridization between two samples of populations
makefreq

Function to generate allelic frequencies
SequencesToGenind

Importing data from an alignement of sequences to a genind object
dapc

Discriminant Analysis of Principal Components (DAPC)
Accessors

Accessors for adegenet objects
read.genetix

Reading data from GENETIX
read.fstat

Reading data from Fstat
selPopSize

Select genotypes of well-represented populations
export

Conversion functions from adegenet to other R packages