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adegenet (version 1.2-8)

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

11,337

Version

1.2-8

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

November 4th, 2010

Functions in adegenet (1.2-8)

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

H3N2

Seasonal influenza (H3N2) HA segment data

haploGen

Simulation of genealogies of haplotypes

a-score

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

import

Importing data from several softwares to a genind object

old2new

Convert objects with obsolete classe into new objects

read.fstat

Reading data from Fstat

dapcIllus

Simulated data illustrating the DAPC

chooseCN

Function to choose a connection network

global.rtest

Global and local tests

hybridize

Simulated hybridization between two samples of populations

genind2genpop

Conversion from a genind to a genpop object

as methods in adegenet

Converting genind/genpop objects to other classes

monmonier

Boundary detection using Monmonier algorithm

nancycats

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

dist.genpop

Genetic distances between populations

rupica

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

sim2pop

Simulated genotypes of two georeferenced populations

genind class

adegenet formal class (S4) for individual genotypes

haploPop

Simulation of populations of haplotypes

spca

Spatial principal component analysis

gstat.randtest

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

na.replace-methods

Replace missing values (NA) from an object

read.structure

Reading data from STRUCTURE

spcaIllus

Simulated data illustrating the sPCA

genpop class

adegenet formal class (S4) for allele counts in populations

coords.monmonier

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

genind constructor

eHGDP

Extended HGDP-CEPH dataset

truenames

Restore true labels of an object

seppop

Separate genotypes per population

scaleGen-methods

Compute scaled allele frequencies

SequencesToGenind

Importing data from an alignement of sequences to a genind object

selPopSize

Select genotypes of well-represented populations

F statistics

F statistics for genind objects

seploc

Separate data per locus

propTyped-methods

Compute the proportion of typed elements

microbov

Microsatellites genotypes of 15 cattle breeds

Accessors

Accessors for adegenet objects

find.clusters

find.cluster: cluster identification using successive K-means

virtualClasses

Virtual classes for adegenet

adegenet-package

The adegenet package

export

Conversion functions from adegenet to other R packages

seqTrack

SeqTrack algorithm for reconstructing genealogies

loadingplot

Represents a cloud of points with colors

colorplot

Represents a cloud of points with colors

df2genind

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

Expected heterozygosity

isPoly-methods

Assess polymorphism in genind/genpop objects

genpop constructor

read.genetix

Reading data from GENETIX

dapc

Discriminant Analysis of Principal Components (DAPC)

propShared

Compute proportion of shared alleles

repool

Pool several genotypes into a single dataset

Auxiliary functions

Utilities functions for adegenet

read.genepop

Reading data from Genepop

makefreq

Function to generate allelic frequencies