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adegenet (version 1.3-4)

adegenet: an R package for the exploratory analysis of genetic and genomic data.

Description

Classes and functions for genetic data analysis within the multivariate framework.

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Version

Install

install.packages('adegenet')

Monthly Downloads

13,063

Version

1.3-4

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

January 18th, 2012

Functions in adegenet (1.3-4)

haploGen

Simulation of genealogies of haplotypes

dist.genpop

Genetic distances between populations

genind constructor

sim2pop

Simulated genotypes of two georeferenced populations

SNPbin-class

Formal class "SNPbin"

glPlot

Plotting genlight objects

isPoly-methods

Assess polymorphism in genind/genpop objects

as.SNPbin

Conversion to class "SNPbin"

genpop class

adegenet formal class (S4) for allele counts in populations

makefreq

Function to generate allelic frequencies

genpop constructor

dapc

Discriminant Analysis of Principal Components (DAPC)

find.clusters

find.cluster: cluster identification using successive K-means

as.genlight

Conversion to class "genlight"

hybridize

Simulated hybridization between two samples of populations

colorplot

Represents a cloud of points with colors

seppop

Separate genotypes per population

genlight-class

Formal class "genlight"

read.fstat

Reading data from Fstat

repool

Pool several genotypes into a single dataset

microbov

Microsatellites genotypes of 15 cattle breeds

eHGDP

Extended HGDP-CEPH dataset

a-score

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

H3N2

Seasonal influenza (H3N2) HA segment data

read.genetix

Reading data from GENETIX

import

Importing data from several softwares to a genind object

SequencesToGenind

Importing data from an alignement of sequences to a genind object

loadingplot

Represents a cloud of points with colors

propTyped-methods

Compute the proportion of typed elements

chooseCN

Function to choose a connection network

dapcIllus

Simulated data illustrating the DAPC

read.snp

Reading Single Nucleotide Polymorphism data

df2genind

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

old2new

Convert objects with obsolete classe into new objects

Expected heterozygosity

genind class

adegenet formal class (S4) for individual genotypes

spcaIllus

Simulated data illustrating the sPCA

Inbreeding estimation

Likelihood-based estimation of inbreeding

genlight auxiliary functions

Auxiliary functions for genlight objects

spca

Spatial principal component analysis

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

monmonier

Boundary detection using Monmonier algorithm

read.structure

Reading data from STRUCTURE

export

Conversion functions from adegenet to other R packages

Auxiliary functions

Utilities functions for adegenet

glSim

Simulation of simple genlight objects

virtualClasses

Virtual classes for adegenet

genind2genpop

Conversion from a genind to a genpop object

seqTrack

SeqTrack algorithm for reconstructing genealogies

haploPop

Simulation of populations of haplotypes

global.rtest

Global and local tests

seploc

Separate data per locus

read.PLINK

Reading PLINK Single Nucleotide Polymorphism data

scaleGen-methods

Compute scaled allele frequencies

coords.monmonier

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

nancycats

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

gstat.randtest

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

propShared

Compute proportion of shared alleles

na.replace-methods

Replace missing values (NA) from an object

adegenet-package

The adegenet package

as methods in adegenet

Converting genind/genpop objects to other classes

Accessors

Accessors for adegenet objects

fasta2genlight

Extract Single Nucleotide Polymorphism (SNPs) from alignments

selPopSize

Select genotypes of well-represented populations

rupica

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

F statistics

F statistics for genind objects

glPca

Principal Component Analysis for genlight objects

truenames

Restore true labels of an object

dapc graphics

Graphics for Discriminant Analysis of Principal Components (DAPC)

read.genepop

Reading data from Genepop