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adegenet (version 1.2-7)

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

16,422

Version

1.2-7

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

October 29th, 2010

Functions in adegenet (1.2-7)

genpop constructor

genpop constructor
adegenet-package

The adegenet package
gstat.randtest

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

Hardy-Weinberg Equilibrium test for multilocus data
monmonier

Boundary detection using Monmonier algorithm
genind2genpop

Conversion from a genind to a genpop object
Hs

Expected heterozygosity
a-score

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

genind constructor
read.fstat

Reading data from Fstat
repool

Pool several genotypes into a single dataset
export

Conversion functions from adegenet to other R packages
nancycats

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

Function to choose a connection network
dapc

Discriminant Analysis of Principal Components (DAPC)
Accessors

Accessors for adegenet objects
find.clusters

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

Simulated hybridization between two samples of populations
eHGDP

Extended HGDP-CEPH dataset
SequencesToGenind

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

Importing data from several softwares to a genind object
makefreq

Function to generate allelic frequencies
dapcIllus

Simulated data illustrating the DAPC
haploPop

Simulation of populations of haplotypes
F statistics

F statistics for genind objects
genind class

adegenet formal class (S4) for individual genotypes
read.genetix

Reading data from GENETIX
colorplot

Represents a cloud of points with colors
isPoly-methods

Assess polymorphism in genind/genpop objects
truenames

Restore true labels of an object
haploGen

Simulation of genealogies of haplotypes
df2genind

Convert a data.frame of genotypes to a genind object, and conversely.
old2new

Convert objects with obsolete classe into new objects
scaleGen-methods

Compute scaled allele frequencies
Auxiliary functions

Utilities functions for adegenet
propTyped-methods

Compute the proportion of typed elements
loadingplot

Represents a cloud of points with colors
na.replace-methods

Replace missing values (NA) from an object
spcaIllus

Simulated data illustrating the sPCA
virtualClasses

Virtual classes for adegenet
rupica

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

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

Compute proportion of shared alleles
seploc

Separate data per locus
microbov

Microsatellites genotypes of 15 cattle breeds
seppop

Separate genotypes per population
H3N2

Seasonal influenza (H3N2) HA segment data
seqTrack

SeqTrack algorithm for reconstructing genealogies
genpop class

adegenet formal class (S4) for allele counts in populations
global.rtest

Global and local tests
sim2pop

Simulated genotypes of two georeferenced populations
read.genepop

Reading data from Genepop
read.structure

Reading data from STRUCTURE
selPopSize

Select genotypes of well-represented populations
as methods in adegenet

Converting genind/genpop objects to other classes
dist.genpop

Genetic distances between populations
spca

Spatial principal component analysis