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adegenet (version 1.2-5)

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

10,375

Version

1.2-5

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

July 29th, 2010

Functions in adegenet (1.2-5)

eHGDP

Extended HGDP-CEPH dataset
haploGen

Simulation of genealogies of haplotypes
HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data
genind constructor

genind constructor
dist.genpop

Genetic distances between populations
export

Conversion functions from adegenet to other R packages
colorplot

Represents a cloud of points with colors
adegenet-package

The adegenet package
import

Importing data from several softwares to a genind object
read.fstat

Reading data from Fstat
Auxiliary functions

Utilities functions for adegenet
genpop class

adegenet formal class (S4) for allele counts in populations
microbov

Microsatellites genotypes of 15 cattle breeds
fstat

F statistics for genind objects
genind2genpop

Conversion from a genind to a genpop object
haploPop

Simulation of populations of haplotypes
gstat.randtest

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

Compute scaled allele frequencies
nancycats

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

Simulated hybridization between two samples of populations
dapcIllus

Simulated data illustrating the DAPC
chooseCN

Function to choose a connection network
propShared

Compute proportion of shared alleles
global.rtest

Global and local tests
Hs

Expected heterozygosity
H3N2

Seasonal influenza (H3N2) HA segment data
seploc

Separate data per locus
old2new

Convert objects with obsolete classe into new objects
na.replace-methods

Replace missing values (NA) from an object
dapc

Discriminant Analysis of Principal Components (DAPC)
isPoly-methods

Assess polymorphism in genind/genpop objects
read.structure

Reading data from STRUCTURE
propTyped-methods

Compute the proportion of typed elements
repool

Pool several genotypes into a single dataset
df2genind

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

Separate genotypes per population
read.genetix

Reading data from GENETIX
Accessors

Accessors for adegenet objects
seqTrack

SeqTrack algorithm for reconstructing genealogies
coords.monmonier

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

Virtual classes for adegenet
sim2pop

Simulated genotypes of two georeferenced populations
selPopSize

Select genotypes of well-represented populations
as methods in adegenet

Converting genind/genpop objects to other classes
spcaIllus

Simulated data illustrating the sPCA
SequencesToGenind

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

Restore true labels of an object
genind class

adegenet formal class (S4) for individual genotypes
spca

Spatial principal component analysis
find.clusters

find.cluster: cluster identification using successive K-means
genpop constructor

genpop constructor
makefreq

Function to generate allelic frequencies
monmonier

Boundary detection using Monmonier algorithm
read.genepop

Reading data from Genepop
rupica

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

Represents a cloud of points with colors