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adegenet (version 1.2-6)

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

13,924

Version

1.2-6

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

September 22nd, 2010

Functions in adegenet (1.2-6)

Auxiliary functions

Utilities functions for adegenet

Accessors

Accessors for adegenet objects

eHGDP

Extended HGDP-CEPH dataset

find.clusters

find.cluster: cluster identification using successive K-means

as methods in adegenet

Converting genind/genpop objects to other classes

read.structure

Reading data from STRUCTURE

haploGen

Simulation of genealogies of haplotypes

seploc

Separate data per locus

seppop

Separate genotypes per population

SequencesToGenind

Importing data from an alignement of sequences to a genind object

sim2pop

Simulated genotypes of two georeferenced populations

propTyped-methods

Compute the proportion of typed elements

truenames

Restore true labels of an object

read.genepop

Reading data from Genepop

chooseCN

Function to choose a connection network

H3N2

Seasonal influenza (H3N2) HA segment data

genpop constructor

export

Conversion functions from adegenet to other R packages

hybridize

Simulated hybridization between two samples of populations

adegenet-package

The adegenet package

genind2genpop

Conversion from a genind to a genpop object

dist.genpop

Genetic distances between populations

microbov

Microsatellites genotypes of 15 cattle breeds

genind constructor

seqTrack

SeqTrack algorithm for reconstructing genealogies

df2genind

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

haploPop

Simulation of populations of haplotypes

genind class

adegenet formal class (S4) for individual genotypes

makefreq

Function to generate allelic frequencies

dapcIllus

Simulated data illustrating the DAPC

read.genetix

Reading data from GENETIX

gstat.randtest

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

genpop class

adegenet formal class (S4) for allele counts in populations

na.replace-methods

Replace missing values (NA) from an object

read.fstat

Reading data from Fstat

selPopSize

Select genotypes of well-represented populations

coords.monmonier

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

repool

Pool several genotypes into a single dataset

scaleGen-methods

Compute scaled allele frequencies

loadingplot

Represents a cloud of points with colors

monmonier

Boundary detection using Monmonier algorithm

F statistics

F statistics for genind objects

spca

Spatial principal component analysis

nancycats

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

dapc

Discriminant Analysis of Principal Components (DAPC)

old2new

Convert objects with obsolete classe into new objects

colorplot

Represents a cloud of points with colors

propShared

Compute proportion of shared alleles

rupica

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

spcaIllus

Simulated data illustrating the sPCA

isPoly-methods

Assess polymorphism in genind/genpop objects

import

Importing data from several softwares to a genind object

virtualClasses

Virtual classes for adegenet

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

global.rtest

Global and local tests

Expected heterozygosity