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adegenet (version 1.3-2)

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

11,337

Version

1.3-2

License

GPL (>= 2)

Maintainer

Thibaut Jombart

Last Published

November 10th, 2011

Functions in adegenet (1.3-2)

glPlot

Plotting genlight objects

na.replace-methods

Replace missing values (NA) from an object

glPca

Principal Component Analysis for genlight objects

as.SNPbin

Conversion to class "SNPbin"

truenames

Restore true labels of an object

genind2genpop

Conversion from a genind to a genpop object

SNPbin-class

Formal class "SNPbin"

dist.genpop

Genetic distances between populations

Auxiliary functions

Utilities functions for adegenet

chooseCN

Function to choose a connection network

propTyped-methods

Compute the proportion of typed elements

colorplot

Represents a cloud of points with colors

microbov

Microsatellites genotypes of 15 cattle breeds

propShared

Compute proportion of shared alleles

as methods in adegenet

Converting genind/genpop objects to other classes

H3N2

Seasonal influenza (H3N2) HA segment data

HWE.test.genind

Hardy-Weinberg Equilibrium test for multilocus data

glSim

Simulation of simple genlight objects

spca

Spatial principal component analysis

import

Importing data from several softwares to a genind object

read.PLINK

Reading PLINK Single Nucleotide Polymorphism data

hybridize

Simulated hybridization between two samples of populations

dapc

Discriminant Analysis of Principal Components (DAPC)

adegenet-package

The adegenet package

repool

Pool several genotypes into a single dataset

Inbreeding estimation

Likelihood-based estimation of inbreeding

F statistics

F statistics for genind objects

dapcIllus

Simulated data illustrating the DAPC

as.genlight

Conversion to class "genlight"

loadingplot

Represents a cloud of points with colors

isPoly-methods

Assess polymorphism in genind/genpop objects

haploPop

Simulation of populations of haplotypes

genind constructor

seploc

Separate data per locus

rupica

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

selPopSize

Select genotypes of well-represented populations

fasta2genlight

Extract Single Nucleotide Polymorphism (SNPs) from alignments

read.genetix

Reading data from GENETIX

seqTrack

SeqTrack algorithm for reconstructing genealogies

genind class

adegenet formal class (S4) for individual genotypes

genlight-class

Formal class "genlight"

monmonier

Boundary detection using Monmonier algorithm

makefreq

Function to generate allelic frequencies

global.rtest

Global and local tests

export

Conversion functions from adegenet to other R packages

read.genepop

Reading data from Genepop

read.fstat

Reading data from Fstat

genpop class

adegenet formal class (S4) for allele counts in populations

virtualClasses

Virtual classes for adegenet

read.structure

Reading data from STRUCTURE

genpop constructor

read.snp

Reading Single Nucleotide Polymorphism data

a-score

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

eHGDP

Extended HGDP-CEPH dataset

find.clusters

find.cluster: cluster identification using successive K-means

Accessors

Accessors for adegenet objects

sim2pop

Simulated genotypes of two georeferenced populations

seppop

Separate genotypes per population

gstat.randtest

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

haploGen

Simulation of genealogies of haplotypes

SequencesToGenind

Importing data from an alignement of sequences to a genind object

dapc graphics

Graphics for Discriminant Analysis of Principal Components (DAPC)

scaleGen-methods

Compute scaled allele frequencies

df2genind

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

nancycats

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

coords.monmonier

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

old2new

Convert objects with obsolete classe into new objects

Expected heterozygosity

genlight auxiliary functions

Auxiliary functions for genlight objects

spcaIllus

Simulated data illustrating the sPCA