Package: adegenet 2.1.10
Zhian N. Kamvar
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.
Authors:
adegenet_2.1.10.tar.gz
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adegenet.pdf |adegenet.html✨
adegenet/json (API)
| # Install 'adegenet' in R: |
| install.packages('adegenet', repos = c('https://thibautjombart.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thibautjombart/adegenet/issues
- H3N2 - Seasonal influenza (H3N2) HA segment data
- dapcIllus - Simulated data illustrating the DAPC
- eHGDP - Extended HGDP-CEPH dataset
- hybridtoy - Toy hybrid dataset
- microbov - Microsatellites genotypes of 15 cattle breeds
- nancycats - Microsatellites genotypes of 237 cats from 17 colonies of Nancy
- rupica - Microsatellites genotypes of 335 chamois
- sim2pop - Simulated genotypes of two georeferenced populations
- spcaIllus - Simulated data illustrating the sPCA
- swallowtails - Microsatellites genotypes of 781 swallowtail butterflies from 40 populations in Alberta and British Columbia, Canada
Last updated 2 years agofrom:bb8b9e8967. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 15 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 15 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 15 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 15 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 15 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 15 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 15 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 15 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 15 2024 |
Exports:.genlab.internal_C_routines.readExt.render.server.info.rmspaces[.haploGena.scoreaddStrataaddStrata<-adegenetIssuesadegenetServeradegenetTutorialadegenetWebAIC.snapclustAICcAICc.snapclustalignment2genindallelesalleles<-any2colas.data.frame.genindas.data.frame.genlightas.data.frame.genpopas.genindas.genlightas.genpopas.genpop.genindas.igraph.haploGenas.igraph.seqTrackas.integer.SNPbinas.ktab.genindas.ktab.genpopas.ldaas.lda.dapcas.list.genlightas.matrixas.matrix.genindas.matrix.genlightas.matrix.genpopas.POSIXct.haploGenas.seqTrack.haploGenas.SNPbinassignplotazurBIC.snapclustbluepalbytesToBinIntbytesToIntc.SNPbincbind.genlightcbind.SNPbinCheckAllSegcheckTypechooseCNchrchr<-chromosomechromosome<-colorplotcolorplot.defaultcolorplot.spcacompoplotcompoplot.dapccompoplot.matrixcompoplot.snapclustcoords.monmoniercornerdapcdapc.data.framedapc.dudidapc.geninddapc.genlightdapc.matrixdeepseasundf2geninddist.genpopDNAbin2genindexport_to_mvmapperexport_to_mvmapper.dapcexport_to_mvmapper.defaultexport_to_mvmapper.dudiexport_to_mvmapper.spcaextract.PLINKmapfac2colfasta2DNAbinfasta2genlightfind.clustersfind.clusters.data.framefind.clusters.genindfind.clusters.genlightfind.clusters.matrixfindMutationsfindMutations.DNAbinflamefunkygengraphgengraph.defaultgengraph.distgengraph.DNAbingengraph.genindgengraph.genpopgengraph.matrixgenindgenind2dfgenind2genpopgenpopget.likelihoodget.likelihood.seqTrackglDotProdGLdotProdglMeanglNAglobal.rtestglPcaglPlotglSimglSumGLsumFreqGLsumIntglVargraphMutationsgraphMutations.DNAbingreenpalgreypalhaploGenhierhier<-HsHs.testHWE.test.genindhybridizehybridpalimport2genindinbreedingindNamesindNames<-initializeis.genindis.genpopisPolyKICKIC.snapclustlabels.haploGenlightseasunloadingplotloadingplot.defaultloadingplot.glPcalocal.rtestlocFaclocNameslocNames<-makefreqminorAllelemonmonierNA.posinAllnameStratanameStrata<-nb_shared_allnIndnLocnPopnum2colold2new_genindold2new_genlightold2new_genpopoptim.a.scoreoptimize.monmonierotherother<-pairDistpairDist.defaultpairDistPlotpairDistPlot.defaultpairDistPlot.distpairDistPlot.DNAbinpairDistPlot.genindpairDistPlot.matrixploidyploidy<-plotplot.haploGenplot.monmonierplot.seqTrackplot.spcaplotHaploGenplotSeqTrackpoppop<-popNamespopNames<-positionposition<-predict.dapcprint.dapcprint.genindSummaryprint.genpopSummaryprint.glPcaprint.haploGenprint.monmonierprint.spcapropSharedpropTypedrbind.genlightread.fstatread.genepopread.genetixread.PLINKread.snpread.structureredpalrepoolsample.haploGenscaleGenscatter.dapcscatter.glPcascreeplot.spcaseasunselPopSizeseplocseppopseqTrackseqTrack.defaultseqTrack.haploGenseqTrack.matrixsetPopsetPop<-showmekittenssnapclustsnapclust.choose.ksnpposi.plotsnpposi.plot.DNAbinsnpposi.plot.integersnpposi.plot.numericsnpposi.testsnpposi.test.DNAbinsnpposi.test.integersnpposi.test.numericsnpzipspcaspca_randtestspca.data.framespca.defaultspca.genindspca.genpopspca.matrixspectralsplitStratasplitStrata<-stratastrata<-summarysummary.dapcsummary.spcatabtransptruenamesviridwaspxvalDapcxvalDapc.data.framexvalDapc.defaultxvalDapc.genindxvalDapc.genlightxvalDapc.matrix
Dependencies:ade4apebase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtablehtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepermutepillarpixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangsassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vctrsveganviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Internal C routines | .internal_C_routines binIntToBytes bytesToBinInt bytesToInt CheckAllSeg GLdotProd GLsumFreq GLsumInt nb_shared_all |
| Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC) | a.score optim.a.score |
| Accessors for adegenet objects | $,genind-method $,genpop-method $<-,genind-method $<-,genpop-method alleles alleles,gen-method alleles,genind-method alleles,genpop-method alleles<- alleles<-,gen-method alleles<-,genind-method alleles<-,genpop-method indNames indNames,genind-method indNames<- indNames<-,genind-method locFac locFac,gen-method locFac,genind-method locFac,genpop-method locNames locNames,gen-method locNames,genind-method locNames,genpop-method locNames<- locNames<-,gen-method locNames<-,genind-method locNames<-,genpop-method nAll nAll,gen-method nAll,genind-method nAll,genpop-method nInd nInd,genind-method nLoc nLoc,gen-method nLoc,genind-method nLoc,genpop-method nPop nPop,genind-method nPop,genpop-method other other,gen-method other,genind-method other,genpop-method other<- other<-,gen-method other<-,genind-method other<-,genpop-method ploidy ploidy,genind-method ploidy,genpop-method ploidy<- ploidy<-,genind-method ploidy<-,genpop-method pop pop,genind-method pop<- pop<-,gen-method pop<-,genind-method popNames popNames,genind-method popNames,genpop-method popNames<- popNames<-,genind-method popNames<-,genpop-method [,genind,ANY,ANY,ANY-method [,genind-method [,genpop,ANY,ANY,ANY-method [,genpop-method |
| Web servers for adegenet | adegenetServer |
| The adegenet package | adegenet adegenet.package |
| Functions to access online resources for adegenet | adegenetIssues adegenetTutorial adegenetWeb |
| Compute Akaike Information Criterion (AIC) for snapclust | AIC.snapclust |
| Compute Akaike Information Criterion for small samples (AICc) for snapclust | AICc AICc.snapclust |
| Converting genind/genpop objects to other classes | as,genind,data.frame-method as,genind,genpop-method as,genind,ktab-method as,genind,matrix-method as,genpop,data.frame-method as,genpop,ktab-method as,genpop,matrix-method as-method as.data.frame.genind as.data.frame.genpop as.genpop.genind as.ktab.genind as.ktab.genpop as.matrix.genind as.matrix.genpop coerce,genind,data.frame-method coerce,genind,genpop-method coerce,genind,ktab-method coerce,genind,matrix-method coerce,genpop,data.frame-method coerce,genpop,ktab-method coerce,genpop,matrix-method ktab-class |
| Conversion to class "genlight" | as,genlight,data.frame-method as,genlight,list-method as,genlight,matrix-method as.genlight as.genlight,data.frame-method as.genlight,list-method as.genlight,matrix-method coerce,genlight,data.frame-method coerce,genlight,list-method coerce,genlight,matrix-method |
| Conversion to class "SNPbin" | as,SNPbin,integer-method as,SNPbin,numeric-method as.SNPbin as.SNPbin,integer-method as.SNPbin,numeric-method coerce,integer,SNPbin-method coerce,numeric,SNPbin-method |
| Auxiliary functions for adegenet | .genlab .readExt .rmspaces any2col azur bluepal checkType corner deepseasun fac2col flame funky greenpal greypal hybridpal lightseasun num2col redpal seasun spectral transp virid wasp |
| Compute Bayesian Information Criterion (BIC) for snapclust | BIC.snapclust |
| Function to choose a connection network | chooseCN |
| Represents a cloud of points with colors | colorplot colorplot.default |
| Genotype composition plot | compoplot compoplot.dapc compoplot.matrix compoplot.snapclust |
| Returns original points in results paths of an object of class 'monmonier' | coords.monmonier |
| Discriminant Analysis of Principal Components (DAPC) | as.lda as.lda.dapc dapc dapc.data.frame dapc.dudi dapc.genind dapc.genlight dapc.matrix predict.dapc print.dapc summary.dapc |
| Cross-validation for Discriminant Analysis of Principal Components (DAPC) | xvalDapc xvalDapc.data.frame xvalDapc.default xvalDapc.genind xvalDapc.genlight xvalDapc.matrix |
| Graphics for Discriminant Analysis of Principal Components (DAPC) | assignplot scatter.dapc |
| Simulated data illustrating the DAPC | dapcIllus |
| Convert a data.frame of allele data to a genind object. | df2genind |
| Genetic distances between populations | dist.genpop |
| Extended HGDP-CEPH dataset | eHGDP |
| Export analysis for mvmapper visualisation | export_to_mvmapper export_to_mvmapper.dapc export_to_mvmapper.default export_to_mvmapper.dudi export_to_mvmapper.spca |
| Reading PLINK Single Nucleotide Polymorphism data | extract.PLINKmap read.PLINK read.plink |
| Read large DNA alignments into R | fasta2DNAbin |
| Extract Single Nucleotide Polymorphism (SNPs) from alignments | fasta2genlight |
| find.cluster: cluster identification using successive K-means | .find.sub.clusters find.clusters find.clusters.data.frame find.clusters.genind find.clusters.genlight find.clusters.matrix |
| Identify mutations between DNA sequences | findMutations findMutations.DNAbin graphMutations graphMutations.DNAbin |
| Genetic transitive graphs | gengraph gengraph.default gengraph.dist gengraph.DNAbin gengraph.genind gengraph.genpop gengraph.matrix |
| adegenet formal class (S4) for individual genotypes | .valid.genind genind-class is.genind names,genind-method print,genind-method print,genindSummary-method print.genindSummary show,genind-method summary,genind-method |
| Convert a genind object to a data.frame. | genind2df |
| Conversion from a genind to a genpop object | genind2genpop |
| Auxiliary functions for genlight objects | glDotProd glMean glNA glSum glVar |
| Formal class "genlight" | $,genlight-method $<-,genlight-method alleles,genlight-method alleles<-,genlight-method as,data.frame,genlight-method as,list,genlight-method as,matrix,genlight-method as.data.frame.genlight as.list.genlight as.matrix.genlight cbind.genlight chr chr,genlight-method chr<- chr<-,genlight-method chromosome chromosome,genlight-method chromosome<- chromosome<-,genlight-method coerce,data.frame,genlight-method coerce,list,genlight-method coerce,matrix,genlight-method dim,genlight-method genlight genlight-class indNames,genlight-method indNames<-,genlight-method initialize,genlight-method locNames,genlight-method locNames<-,genlight-method NA.posi NA.posi,genlight-method names,genlight-method nInd,genlight-method nLoc,genlight-method nPop,genlight-method other,genlight-method other<-,genlight-method ploidy,genlight-method ploidy<-,genlight-method pop,genlight-method pop<-,genlight-method popNames,genlight-method popNames<-,genlight-method position position,genlight-method position<- position<-,genlight-method rbind.genlight show,genlight-method tab,genlight-method [,genlight,ANY,ANY,ANY-method [,genlight,ANY,ANY-method [,genlight-method |
| adegenet formal class (S4) for allele counts in populations | dist,genpop,ANY,ANY,ANY,missing-method genpop-class is.genpop names,genpop-method print,genpopSummary-method print.genpopSummary show,genpop-method summary,genpop-method |
| Global and local tests | global.rtest local.rtest |
| Principal Component Analysis for genlight objects | glPca loadingplot.glPca print.glPca scatter.glPca |
| Plotting genlight objects | glPlot plot,genlight,ANY-method plot,genlight-method plot.genlight |
| Simulation of simple genlight objects | glSim |
| Seasonal influenza (H3N2) HA segment data | H3N2 USflu usflu USflu.fasta usflu.fasta |
| Simulation of genealogies of haplotypes | as.igraph.haploGen as.POSIXct.haploGen as.seqTrack.haploGen haploGen haploGen-class labels.haploGen plot.haploGen plotHaploGen print.haploGen sample.haploGen seqTrack.haploGen [.haploGen |
| Access and manipulate the population hierarchy for genind or genlight objects. | hier hier,genind-method hier,genlight-method hier<- hier<-,genind-method hier<-,genlight-method |
| Expected heterozygosity (Hs) | Hs |
| Test differences in expected heterozygosity (Hs) | Hs.test |
| Hardy-Weinberg Equilibrium test for multilocus data | HWE.test.genind |
| Function hybridize takes two genind in inputs and generates hybrids individuals having one parent in both objects. | hybridize |
| Toy hybrid dataset | hybridtoy |
| Importing data from several softwares to a genind object | import2genind |
| Likelihood-based estimation of inbreeding | inbreeding |
| genind constructor | as.genind genind initialize,genind-method initialize,genind-methods |
| genpop constructor | as.genpop genpop initialize,genpop-method initialize,genpop-methods |
| Assess polymorphism in genind/genpop objects | isPoly isPoly,genind-method isPoly,genpop-method isPoly-methods |
| Compute Akaike Information Criterion for small samples (AICc) for snapclust | KIC KIC.snapclust |
| Represents a cloud of points with colors | loadingplot loadingplot.default |
| Compute allelic frequencies | makefreq makefreq,genind-method makefreq,genind-methods makefreq,genpop-method makefreq,genpop-methods makefreq.genind makefreq.genpop |
| Microsatellites genotypes of 15 cattle breeds | microbov |
| Compute minor allele frequency | minorAllele |
| Boundary detection using Monmonier algorithm | monmonier optimize.monmonier plot.monmonier print.monmonier |
| Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France) | nancycats |
| Convert objects with obsolete classes into new objects | old2new old2new_genind old2new_genlight old2new_genpop |
| Pairwise distance plots | pairDist pairDist.default pairDistPlot pairDistPlot.default pairDistPlot.dist pairDistPlot.DNAbin pairDistPlot.genind pairDistPlot.matrix |
| Compute proportion of shared alleles | propShared |
| Compute the proportion of typed elements | propTyped propTyped,genind-method propTyped,genpop-method propTyped-methods |
| Reading data from Fstat | read.fstat |
| Reading data from Genepop | read.genepop |
| Reading data from GENETIX | read.genetix |
| Reading Single Nucleotide Polymorphism data | read.snp |
| Reading data from STRUCTURE | read.structure |
| Pool several genotypes into a single dataset | repool |
| Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France) | rupica |
| Compute scaled allele frequencies | scaleGen scaleGen,genind-method scaleGen,genpop-method scaleGen-methods |
| Select genotypes of well-represented populations | selPopSize selPopSize,ANY-method selPopSize,genind-method selPopSize-methods |
| Separate data per locus | seploc seploc,ANY-method seploc,genind-method seploc,genlight-method seploc,genpop-method seploc-methods |
| Separate genotypes per population | seppop seppop,ANY-method seppop,genind-method seppop,genlight-method seppop-methods |
| SeqTrack algorithm for reconstructing genealogies | as.igraph.seqTrack get.likelihood get.likelihood.seqTrack plot.seqTrack plotSeqTrack seqTrack seqTrack-class seqTrack.default seqTrack.matrix |
| Importing data from an alignement of sequences to a genind object | alignment2genind DNAbin2genind |
| Manipulate the population factor of genind objects. | setPop setPop,genind-method setPop,genlight-method setPop<- setPop<-,genind-method setPop<-,genlight-method |
| When you need a break... | showmekittens |
| Simulated genotypes of two georeferenced populations | sim2pop |
| Maximum-likelihood genetic clustering using EM algorithm | snapclust |
| Choose the number of clusters for snapclust using AIC, BIC or AICc | snapclust.choose.k |
| Formal class "SNPbin" | $,SNPbin-method $<-,SNPbin-method as,integer,SNPbin-method as,numeric,SNPbin-method as.integer.SNPbin c.SNPbin cbind.SNPbin coerce,SNPbin,integer-method initialize,SNPbin-method NA.posi,SNPbin-method names,SNPbin-method nLoc,SNPbin-method ploidy,SNPbin-method ploidy<-,SNPbin-method show,SNPbin-method SNPbin SNPbin-class [,SNPbin,ANY,ANY,ANY-method [,SNPbin,ANY,ANY-method [,SNPbin-method |
| Analyse the position of polymorphic sites | snpposi.plot snpposi.plot.DNAbin snpposi.plot.integer snpposi.plot.numeric snpposi.test snpposi.test.DNAbin snpposi.test.integer snpposi.test.numeric |
| Identification of structural SNPs | snpzip |
| Spatial principal component analysis | colorplot.spca plot.spca print.spca screeplot.spca spca spca.data.frame spca.default spca.genind spca.genpop spca.matrix summary.spca |
| Monte Carlo test for sPCA | spca_randtest |
| Simulated data illustrating the sPCA | spcaIllus |
| Access and manipulate the population strata for genind or genlight objects. | addStrata addStrata,genind-method addStrata,genlight-method addStrata<- addStrata<-,genind-method addStrata<-,genlight-method nameStrata nameStrata,genind-method nameStrata,genlight-method nameStrata<- nameStrata<-,genind-method nameStrata<-,genlight-method splitStrata splitStrata,genind-method splitStrata,genlight-method splitStrata<- splitStrata<-,genind-method splitStrata<-,genlight-method strata strata,genind-method strata,genlight-method strata<- strata<-,genind-method strata<-,genlight-method |
| Microsatellites genotypes of 781 swallowtail butterflies from 40 populations in Alberta and British Columbia, Canada | swallowtails |
| Access allele counts or frequencies | tab tab,genind-method tab,genind-methods tab,genpop-method tab,genpop-methods tab.genind tab.genpop |
| Restore true labels of an object | truenames truenames,ANY-method truenames,genind-method truenames,genpop-method truenames-methods |
| Virtual classes for adegenet | callOrNULL-class charOrNULL-class dfOrNULL-class factorOrNULL-class formOrNULL-class gen-class indInfo-class intOrNULL-class intOrNum-class listOrNULL-class popInfo-class |
