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adegenet (version 1.3-5)

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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Install

install.packages('adegenet')

Monthly Downloads

16,422

Version

1.3-5

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

November 1st, 2012

Functions in adegenet (1.3-5)

genpop class

adegenet formal class (S4) for allele counts in populations

Expected heterozygosity

propTyped-methods

Compute the proportion of typed elements

H3N2

Seasonal influenza (H3N2) HA segment data

find.clusters

find.cluster: cluster identification using successive K-means

as.SNPbin

Conversion to class "SNPbin"

SNPbin-class

Formal class "SNPbin"

a-score

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

read.PLINK

Reading PLINK Single Nucleotide Polymorphism data

as methods in adegenet

Converting genind/genpop objects to other classes

genind2genpop

Conversion from a genind to a genpop object

coords.monmonier

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

na.replace-methods

Replace missing values (NA) from an object

fasta2genlight

Extract Single Nucleotide Polymorphism (SNPs) from alignments

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

read.genepop

Reading data from Genepop

global.rtest

Global and local tests

read.genetix

Reading data from GENETIX

loadingplot

Represents a cloud of points with colors

scaleGen-methods

Compute scaled allele frequencies

F statistics

F statistics for genind objects

repool

Pool several genotypes into a single dataset

genind constructor

monmonier

Boundary detection using Monmonier algorithm

sim2pop

Simulated genotypes of two georeferenced populations

as.genlight

Conversion to class "genlight"

Auxiliary functions

Auxiliary functions for adegenet

export

Conversion functions from adegenet to other R packages

microbov

Microsatellites genotypes of 15 cattle breeds

adegenet-package

The adegenet package

seqTrack

SeqTrack algorithm for reconstructing genealogies

genlight auxiliary functions

Auxiliary functions for genlight objects

dapc

Discriminant Analysis of Principal Components (DAPC)

SequencesToGenind

Importing data from an alignement of sequences to a genind object

chooseCN

Function to choose a connection network

propShared

Compute proportion of shared alleles

gengraph

Genetic transitive graphs

haploPop

Simulation of populations of haplotypes

genpop constructor

read.structure

Reading data from STRUCTURE

rupica

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

genlight-class

Formal class "genlight"

Accessors

Accessors for adegenet objects

df2genind

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

haploGen

Simulation of genealogies of haplotypes

makefreq

Function to generate allelic frequencies

spca

Spatial principal component analysis

import

Importing data from several softwares to a genind object

dapcIllus

Simulated data illustrating the DAPC

seploc

Separate data per locus

seppop

Separate genotypes per population

hybridize

Simulated hybridization between two samples of populations

glPca

Principal Component Analysis for genlight objects

virtualClasses

Virtual classes for adegenet

glSim

Simulation of simple genlight objects

old2new

Convert objects with obsolete classe into new objects

glPlot

Plotting genlight objects

spcaIllus

Simulated data illustrating the sPCA

fasta2DNAbin

Read large DNA alignments into R

Inbreeding estimation

Likelihood-based estimation of inbreeding

genind class

adegenet formal class (S4) for individual genotypes

selPopSize

Select genotypes of well-represented populations

isPoly-methods

Assess polymorphism in genind/genpop objects

dist.genpop

Genetic distances between populations

eHGDP

Extended HGDP-CEPH dataset

nancycats

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

read.snp

Reading Single Nucleotide Polymorphism data

truenames

Restore true labels of an object

colorplot

Represents a cloud of points with colors

gstat.randtest

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

dapc graphics

Graphics for Discriminant Analysis of Principal Components (DAPC)

read.fstat

Reading data from Fstat