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adegenet (version 1.4-2)

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

11,001

Version

1.4-2

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

May 13th, 2014

Functions in adegenet (1.4-2)

Website and tutorials

Website and tutorials for adegenet

dapcIllus

Simulated data illustrating the DAPC

sim2pop

Simulated genotypes of two georeferenced populations

as.genlight

Conversion to class "genlight"

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

hybridize

Simulated hybridization between two samples of populations

dapc

Discriminant Analysis of Principal Components (DAPC)

read.PLINK

Reading PLINK Single Nucleotide Polymorphism data

H3N2

Seasonal influenza (H3N2) HA segment data

read.snp

Reading Single Nucleotide Polymorphism data

old2new

Convert objects with obsolete classe into new objects

a-score

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

isPoly-methods

Assess polymorphism in genind/genpop objects

haploGen

Simulation of genealogies of haplotypes

chooseCN

Function to choose a connection network

glPca

Principal Component Analysis for genlight objects

import

Importing data from several softwares to a genind object

rupica

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

Inbreeding estimation

Likelihood-based estimation of inbreeding

eHGDP

Extended HGDP-CEPH dataset

dist.genpop

Genetic distances between populations

na.replace-methods

Replace missing values (NA) from an object

Auxiliary functions

Auxiliary functions for adegenet

seppop

Separate genotypes per population

seqTrack

SeqTrack algorithm for reconstructing genealogies

read.genetix

Reading data from GENETIX

genind2genpop

Conversion from a genind to a genpop object

genpop constructor

repool

Pool several genotypes into a single dataset

read.genepop

Reading data from Genepop

as.SNPbin

Conversion to class "SNPbin"

microbov

Microsatellites genotypes of 15 cattle breeds

read.fstat

Reading data from Fstat

Adegenet servers

Web servers for adegenet

propShared

Compute proportion of shared alleles

as methods in adegenet

Converting genind/genpop objects to other classes

SNPbin-class

Formal class "SNPbin"

glSim

Simulation of simple genlight objects

df2genind

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

colorplot

Represents a cloud of points with colors

monmonier

Boundary detection using Monmonier algorithm

Expected heterozygosity

makefreq

Function to generate allelic frequencies

loadingplot

Represents a cloud of points with colors

fasta2genlight

Extract Single Nucleotide Polymorphism (SNPs) from alignments

export

Conversion functions from adegenet to other R packages

fasta2DNAbin

Read large DNA alignments into R

findMutations

Identify mutations between DNA sequences

F statistics

F statistics for genind objects

genlight-class

Formal class "genlight"

genpop class

adegenet formal class (S4) for allele counts in populations

dapc graphics

Graphics for Discriminant Analysis of Principal Components (DAPC)

genind constructor

Accessors

Accessors for adegenet objects

seploc

Separate data per locus

selPopSize

Select genotypes of well-represented populations

genlight auxiliary functions

Auxiliary functions for genlight objects

spcaIllus

Simulated data illustrating the sPCA

genind class

adegenet formal class (S4) for individual genotypes

DAPC cross-validation

Cross-validation for Discriminant Analysis of Principal Components (DAPC)

global.rtest

Global and local tests

nancycats

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

gstat.randtest

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

adegenet-package

The adegenet package

find.clusters

find.cluster: cluster identification using successive K-means

virtualClasses

Virtual classes for adegenet

read.structure

Reading data from STRUCTURE

glPlot

Plotting genlight objects

truenames

Restore true labels of an object

snpposi

Analyse the position of polymorphic sites

spca

Spatial principal component analysis

coords.monmonier

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

propTyped-methods

Compute the proportion of typed elements

gengraph

Genetic transitive graphs

SequencesToGenind

Importing data from an alignement of sequences to a genind object

scaleGen-methods

Compute scaled allele frequencies