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adegenet (version 1.2-3)

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

1.2-3

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

April 3rd, 2009

Functions in adegenet (1.2-3)

coords.monmonier

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

adegenet-package

The adegenet package

microbov

Microsatellites genotypes of 15 cattle breeds

genpop

adegenet formal class (S4) for allele counts in populations

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

isPoly-methods

Assess polymorphism in genind/genpop objects

colorplot

Represents a cloud of points with colors

genind2genpop

Conversion from a genind to a genpop object

Accessors

Accessors for adegenet objects

gstat.randtest

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

export

Conversion functions from adegenet to other R packages

genpop constructor

fstat

F statistics for genind objects

genind

adegenet formal class (S4) for individual genotypes

df2genind

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

na.replace-methods

Replace missing values (NA) from an object

import

Importing data from several softwares to a genind object

chooseCN

Function to choose a connection network

Auxiliary functions

Utilities functions for adegenet

old2new

Convert objects with obsolete classe into new objects

seploc

Separate data per locus

scaleGen-methods

Compute scaled allele frequencies

selPopSize

Select genotypes of well-represented populations

rupica

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

monmonier

Boundary detection using Monmonier algorithm

hybridize

Simulated hybridization between two samples of populations

as methods in adegenet

Converting genind/genpop objects to other classes

spcaIllus

Simulated data illustrating the sPCA

read.genetix

Reading data from GENETIX

propTyped-methods

Compute the proportion of typed elements

truenames

Restore true labels of an object

spca

Spatial principal component analysis

genind constructor

sim2pop

Simulated genotypes of two georeferenced populations

read.structure

Reading data from STRUCTURE

virtualClasses

Virtual classes for adegenet

propShared

Compute proportion of shared alleles

loadingplot

Represents a cloud of points with colors

global.rtest

Global and local tests

read.fstat

Reading data from Fstat

nancycats

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

repool

Pool several genotypes into the same dataset

seppop

Separate genotypes per population

read.genepop

Reading data from Genepop

makefreq

Function to generate allelic frequencies

dist.genpop

Genetic distances between populations

SequencesToGenind

Importing data from an alignement of sequences to a genind object