adegenet: Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

AuthorThibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie- Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne Cori, Federico Calboli
Date of publication2016-02-15 16:12:41
MaintainerThibaut Jombart <thibautjombart@gmail.com>
LicenseGPL (>= 2)
Version2.0.1
http://adegenet.r-forge.r-project.org/

View on CRAN

Man pages

accessors: Accessors for adegenet objects

adegenet.package: The adegenet package

ascore: Compute and optimize a-score for Discriminant Analysis of...

as.genlight: Conversion to class "genlight"

as-methods: Converting genind/genpop objects to other classes

as.SNPbin: Conversion to class "SNPbin"

auxil: Auxiliary functions for adegenet

chooseCN: Function to choose a connection network

colorplot: Represents a cloud of points with colors

coords.monmonier: Returns original points in results paths of an object of...

dapc: Discriminant Analysis of Principal Components (DAPC)

dapcGraphics: Graphics for Discriminant Analysis of Principal Components...

dapcIllus: Simulated data illustrating the DAPC

df2genind: Convert a data.frame of allele data to a genind object.

dist.genpop: Genetic distances between populations

eHGDP: Extended HGDP-CEPH dataset

fasta2DNAbin: Read large DNA alignments into R

fasta2genlight: Extract Single Nucleotide Polymorphism (SNPs) from alignments

find.clusters: find.cluster: cluster identification using successive K-means

gengraph: Genetic transitive graphs

genind: adegenet formal class (S4) for individual genotypes

genind2df: Convert a genind object to a data.frame.

genind2genpop: Conversion from a genind to a genpop object

genlight: Formal class "genlight"

genpop: adegenet formal class (S4) for allele counts in populations

glAux: Auxiliary functions for genlight objects

glPca: Principal Component Analysis for genlight objects

glPlot: Plotting genlight objects

glSim: Simulation of simple genlight objects

H3N2: Seasonal influenza (H3N2) HA segment data

haploGen: Simulation of genealogies of haplotypes

hierarchy-methods: Access and manipulate the population hierarchy for genind or...

Hs: Expected heterozygosity (Hs)

Hs.test: Test differences in expected heterozygosity (Hs)

HWE: Hardy-Weinberg Equilibrium test for multilocus data

hybridize: Function hybridize takes two genind in inputs and generates...

import2genind: Importing data from several softwares to a genind object

inbreeding: Likelihood-based estimation of inbreeding

isPoly: Assess polymorphism in genind/genpop objects

loadingplot: Represents a cloud of points with colors

makefreq: Compute allelic frequencies

microbov: Microsatellites genotypes of 15 cattle breeds

minorAllele: Compute minor allele frequency

monmonier: Boundary detection using Monmonier algorithm

mutations: Identify mutations between DNA sequences

nancycats: Microsatellites genotypes of 237 cats from 17 colonies of...

new.genind: genind constructor

new.genpop: genpop constructor

old2new: Convert objects with obsolete classes into new objects

pairDist: Pairwise distance plots

population-methods: Manipulate the population factor of genind objects.

propShared: Compute proportion of shared alleles

propTyped: Compute the proportion of typed elements

read.fstat: Reading data from Fstat

read.genepop: Reading data from Genepop

read.genetix: Reading data from GENETIX

read.PLINK: Reading PLINK Single Nucleotide Polymorphism data

read.snp: Reading Single Nucleotide Polymorphism data

read.structure: Reading data from STRUCTURE

repool: Pool several genotypes into a single dataset

rupica: Microsatellites genotypes of 335 chamois (Rupicapra...

scaleGen: Compute scaled allele frequencies

selpopsize: Select genotypes of well-represented populations

seploc: Separate data per locus

seppop: Separate genotypes per population

seqTrack: SeqTrack algorithm for reconstructing genealogies

sequences: Importing data from an alignement of sequences to a genind...

servers: Web servers for adegenet

sim2pop: Simulated genotypes of two georeferenced populations

SNPbin: Formal class "SNPbin"

snpposi: Analyse the position of polymorphic sites

spca: Spatial principal component analysis

spcaIllus: Simulated data illustrating the sPCA

spca.rtests: Global and local tests

strata-methods: Access and manipulate the population strata for genind or...

tab: Access allele counts or frequencies

truenames: Restore true labels of an object

virClasses: Virtual classes for adegenet

web: Functions to access online resources for adegenet

xvalDapc: Cross-validation for Discriminant Analysis of Principal...

Files in this package

adegenet
adegenet/inst
adegenet/inst/CITATION
adegenet/inst/files
adegenet/inst/files/pdH1N1-HA.fasta
adegenet/inst/files/mondata1.rda
adegenet/inst/files/pdH1N1-data.csv
adegenet/inst/files/nancycats.gen
adegenet/inst/files/pdH1N1-NA.fasta
adegenet/inst/files/nancycats.gtx
adegenet/inst/files/exampleSnpDat.snp
adegenet/inst/files/nancycats.str
adegenet/inst/files/usflu.fasta
adegenet/inst/files/nancycats.dat
adegenet/inst/files/AFLP.txt
adegenet/inst/files/mondata2.rda
adegenet/inst/dapcServer
adegenet/inst/dapcServer/ui.R
adegenet/inst/dapcServer/server.R
adegenet/tests
adegenet/tests/testthat.R
adegenet/tests/testthat
adegenet/tests/testthat/test-seppop.R
adegenet/tests/testthat/test-prop.R
adegenet/tests/testthat/test_xval.R
adegenet/tests/testthat/test_import.R
adegenet/tests/testthat/test_summary.R
adegenet/tests/testthat/test_repool.R
adegenet/tests/testthat/test_constructors.R
adegenet/tests/testthat/test_accessors.R
adegenet/tests/testthat/test_hierarchy.R
adegenet/tests/testthat/test_subset.R
adegenet/tests/testthat/test_genlight.R
adegenet/src
adegenet/src/monmonier-utils.c
adegenet/src/GLfunctions.c
adegenet/src/adesub.h
adegenet/src/snpbin.c
adegenet/src/GLfunctions.h
adegenet/src/snpbin.h
adegenet/src/sharedAll.c
adegenet/src/adesub.c
adegenet/NAMESPACE
adegenet/data
adegenet/data/microbov.rda
adegenet/data/dapcIllus.rda
adegenet/data/sim2pop.rda
adegenet/data/H3N2.rda
adegenet/data/nancycats.rda
adegenet/data/rupica.rda
adegenet/data/datalist
adegenet/data/eHGDP.rda
adegenet/data/spcaIllus.rda
adegenet/R
adegenet/R/classes.R adegenet/R/glHandle.R adegenet/R/scale.R adegenet/R/glPlot.R adegenet/R/dapc.R adegenet/R/spca.rtests.R adegenet/R/minorAllele.R adegenet/R/orthobasis.R adegenet/R/basicMethods.R adegenet/R/makefreq.R adegenet/R/accessors.R adegenet/R/handling.R adegenet/R/snpzip.R adegenet/R/xvalDapc.R adegenet/R/genind2genpop.R adegenet/R/simOutbreak.R adegenet/R/inbreeding.R adegenet/R/old2new.R adegenet/R/propTyped.R adegenet/R/strataMethods.R adegenet/R/hybridize.R adegenet/R/chooseCN.R adegenet/R/PCtest.R adegenet/R/adegenet.package.R adegenet/R/import.R adegenet/R/haploPop.R adegenet/R/find.clust.R adegenet/R/sequences.R adegenet/R/haploGen.R adegenet/R/gstat.randtest.R adegenet/R/Hs.R adegenet/R/export.R adegenet/R/coords.monmonier.R adegenet/R/snpposi.R adegenet/R/setAs.R adegenet/R/SNPbin.R adegenet/R/loadingplot.R adegenet/R/fstat.R adegenet/R/hierarchyMethods.R adegenet/R/gengraph.R adegenet/R/colorplot.R adegenet/R/mutations.R adegenet/R/seqTrack.R adegenet/R/glFunctions.R adegenet/R/HWE.R adegenet/R/glSim.R adegenet/R/servers.R adegenet/R/auxil.R adegenet/R/propShared.R adegenet/R/pairDist.R adegenet/R/monmonier.R adegenet/R/datasets.R adegenet/R/zzz.R adegenet/R/constructors.R adegenet/R/spca.R adegenet/R/dist.genpop.R
adegenet/README.md
adegenet/MD5
adegenet/DESCRIPTION
adegenet/ChangeLog
adegenet/man
adegenet/man/as-methods.Rd adegenet/man/spca.Rd adegenet/man/propShared.Rd adegenet/man/import2genind.Rd adegenet/man/haploGen.Rd adegenet/man/population-methods.Rd adegenet/man/new.genpop.Rd adegenet/man/xvalDapc.Rd adegenet/man/selpopsize.Rd adegenet/man/SNPbin.Rd adegenet/man/dist.genpop.Rd adegenet/man/glPlot.Rd adegenet/man/spca.rtests.Rd adegenet/man/microbov.Rd adegenet/man/colorplot.Rd adegenet/man/isPoly.Rd adegenet/man/sim2pop.Rd adegenet/man/adegenet.package.Rd adegenet/man/strata-methods.Rd adegenet/man/snpposi.Rd adegenet/man/fasta2genlight.Rd adegenet/man/read.fstat.Rd adegenet/man/read.genetix.Rd adegenet/man/HWE.Rd adegenet/man/genlight.Rd adegenet/man/web.Rd adegenet/man/hierarchy-methods.Rd adegenet/man/rupica.Rd adegenet/man/spcaIllus.Rd adegenet/man/coords.monmonier.Rd adegenet/man/read.PLINK.Rd adegenet/man/sequences.Rd adegenet/man/hybridize.Rd adegenet/man/inbreeding.Rd adegenet/man/tab.Rd adegenet/man/gengraph.Rd adegenet/man/seppop.Rd adegenet/man/dapcIllus.Rd adegenet/man/nancycats.Rd adegenet/man/loadingplot.Rd adegenet/man/eHGDP.Rd adegenet/man/as.genlight.Rd adegenet/man/monmonier.Rd adegenet/man/new.genind.Rd adegenet/man/Hs.test.Rd adegenet/man/chooseCN.Rd adegenet/man/ascore.Rd adegenet/man/glPca.Rd adegenet/man/old2new.Rd adegenet/man/genind.Rd adegenet/man/makefreq.Rd adegenet/man/virClasses.Rd adegenet/man/glSim.Rd adegenet/man/as.SNPbin.Rd adegenet/man/fasta2DNAbin.Rd adegenet/man/seqTrack.Rd adegenet/man/mutations.Rd adegenet/man/read.snp.Rd adegenet/man/auxil.Rd adegenet/man/repool.Rd adegenet/man/propTyped.Rd adegenet/man/servers.Rd adegenet/man/seploc.Rd adegenet/man/glAux.Rd adegenet/man/dapc.Rd adegenet/man/scaleGen.Rd adegenet/man/Hs.Rd
adegenet/man/snpzip.rd
adegenet/man/genind2df.Rd adegenet/man/genind2genpop.Rd adegenet/man/truenames.Rd adegenet/man/H3N2.Rd adegenet/man/read.genepop.Rd adegenet/man/read.structure.Rd adegenet/man/find.clusters.Rd adegenet/man/genpop.Rd adegenet/man/minorAllele.Rd adegenet/man/accessors.Rd adegenet/man/pairDist.Rd adegenet/man/dapcGraphics.Rd adegenet/man/df2genind.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.