Package: strataG 2.5.01
Eric Archer
strataG: Summaries and Population Structure Analyses of Genetic Data
A toolkit for analyzing stratified population genetic data. Functions are provided for summarizing and checking loci (haploid, diploid, and polyploid), single stranded DNA sequences, calculating most population subdivision metrics, and running external programs such as structure and fastsimcoal. The package is further described in Archer et al (2016) <doi:10.1111/1755-0998.12559>.
Authors:
strataG_2.5.01.tar.gz
strataG_2.5.01.tar.gz(r-4.4-noble)
strataG.pdf |strataG.html✨
strataG/json (API)
| # Install 'strataG' in R: |
| install.packages('strataG', repos = c('https://zkamvar.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ericarcher/stratag/issues
- bowhead.snp.position - Bowhead Whale SNP Genotype Groups
- bowhead.snps - Bowhead Whale SNP Genotypes
- dloop.g - Dolphin dLoop gtypes Object
- dolph.haps - Dolphin mtDNA Haplotype Sequences
- dolph.msats - Dolphin Microsatellite Genotypes
- dolph.seqs - Dolphin mtDNA D-loop Sequences
- dolph.strata - Dolphin Genetic Stratification and Haplotypes
- msats.g - Dolphin Microsatellite gtypes Object
dna-sequencesgeneticslocus-summariesmicrosatellitespopulation-geneticspopulation-genomicspopulation-structuresnp-datasnps
Last updated 6 months agofrom:f38fd47ced. Checks:ERROR: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 25 2024 |
Exports:alleleFreqsalleleSplitallelicRichnessarlequinReadarlequinWritearp2gtypesas.data.frameas.matrixas.multidnabaseFreqsclumppcreateConsensusdf2gtypesdupGenotypesevannoexpandHaplotypesexpectedNumAllelesfixedDifferencesfixedSitesfreq2GenDatafsc2gtypesfscBlock_dnafscBlock_freqfscBlock_microsatfscBlock_snpfscBlock_standardfscCleanupfscDemefscEstParamfscEventfscReadArpfscReadParamEstfscReadSFSfscRunfscSettingsDeffscSettingsDemesfscSettingsEstfscSettingsEventsfscSettingsGeneticsfscSettingsMigrationfscTutorialfscWritefstToNmfusFsgelatogelatoPlotgenepopgenepopWritegenind2gtypesgenlight2gtypesgetAlleleNamesgetDescriptiongetIndNamesgetLociNamesgetNumIndgetNumLocigetNumStratagetOthergetPloidygetSchemesgetSequencesgetStratagetStrataNamesgtypes2genindgtypes2genlightgtypes2locigtypes2phyDatheterozygosityhweTestis.gtypesisTiisTviupacCodeiupacMatjackHWEjackInfluentiallabelHaplotypeslandscape2dflandscape2gtypesLDgenepopldNeloci2gtypeslowFreqSubsmafmafftmaverickRunmostDistantSequencesmostRepresentativeSequencesmRationeiDanucleotideDivergencenucleotideDiversitynumAllelesnumGenotypednumGensEqnumMissingoverallTestpairwiseMatrixpairwiseSummarypairwiseTestpermuteStrataphasephaseFilterphasePosteriorphaseReadPairphaseReadSamplephaseWritephyDat2gtypesprivateAllelespropSharedLocipropUniqueAllelesread.arlequinread.fastaread.megareadGenDataremoveUnusedSequencessequence2gtypessequenceLikelihoodssetDescription<-setOther<-setSchemes<-setStrata<-sfssharedAllelessimGammaHapsstrataSplitstratifystructurePlotstructureReadstructureRunstructureWritesubTypesummarizeAllsummarizeIndssummarizeLocisummarizeSeqssummarytajimasDthetaTiTvRatiotrimNsvalidIupacCodesvariableSiteswrightFstwrite.arlequinwrite.fastawrite.megawrite.nexus.snappwriteGtypes
Dependencies:abindade4adegenetADGofTestapeapexbase64encbootbslibcachemclassclassIntcliclueclustercodacolorspacecommonmarkcopulacpp11crayondata.tableDBIdeldirdigestdplyre1071fansifarverfastmapfastmatchfBasicsfontawesomefsgenepopgenericsggplot2ggrepelgluegridExtragslgssgtablegtoolsHDIntervalhtmltoolshttpuvigraphisobandjquerylibjsonliteKernSmoothkknnlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemodeestmunsellmvtnormnlmenumDerivpcaPPpegaspermutephangornpillarpixmappkgconfigplyrpolyclippromisesproxypsplinepurrrquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppProgressreshape2rlangrmetasimrmutilrpartrunjagss2sassscalessegmentedseqinrsfshinysourcetoolsspspatialspatstat.dataspatstat.geomspatstat.univarspatstat.utilssprexstablestablediststatipstringistringrswfscMisctibbletidyrtidyselecttimeDatetimeSeriesunitsutf8vctrsveganviridisLitewithrwkxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Summaries and population structure analyses of DNA sequence genotypic data | strataG-package strataG |
| Allele Frequencies | alleleFreqs |
| Split Alleles For Diploid Data | alleleSplit |
| Allelic Richness | allelicRichness |
| Read and Write Arlequin Files | arlequin arlequinRead arlequinWrite arp2gtypes read.arlequin write.arlequin |
| Convert 'gtypes' to data.frame or matrix | as.data.frame as.data.frame,gtypes-method as.data.frame.gtypes as.matrix as.matrix,gtypes-method as.matrix.gtypes |
| Convert to multidna | as.multidna |
| Base Frequencies | baseFreqs |
| Bowhead Whale SNP Genotype Groups | bowhead.snp.position |
| Bowhead Whale SNP Genotypes | bowhead.snps |
| Run CLUMPP | clumpp |
| Consensus Sequence | createConsensus |
| Convert a data.frame to gtypes | df2gtypes |
| Dolphin dLoop gtypes Object | dloop.g |
| Dolphin mtDNA Haplotype Sequences | dolph.haps |
| Dolphin Microsatellite Genotypes | dolph.msats |
| Dolphin mtDNA D-loop Sequences | dolph.seqs |
| Dolphin Genetic Stratification and Haplotypes | dolph.strata |
| Duplicate Genotypes | dupGenotypes |
| Run Evanno Method on STRUCTURE Results | evanno |
| Expand Haplotypes | expandHaplotypes |
| Read and Write FASTA | fasta read.fasta write.fasta |
| Fixed Differences | fixedDifferences |
| Fixed Sites | fixedSites |
| Convert Haplotype Frequency Matrices | freq2GenData |
| Input functions for fastsimcoal parameters | fsc.input fscBlock_dna fscBlock_freq fscBlock_microsat fscBlock_snp fscBlock_standard fscDeme fscEstParam fscEvent fscSettings fscSettingsDef fscSettingsDemes fscSettingsEst fscSettingsEvents fscSettingsGenetics fscSettingsMigration |
| Read fastsimcoal output | fsc2gtypes fscRead fscReadArp fscReadParamEst fscReadSFS |
| Run fastsimcoal | fscCleanup fscRun fscTutorial |
| Write fastsimcoal2 input files | fscWrite |
| Fu's Fs | fusFs |
| GELATo - Group ExcLusion and Assignment Test | gelato gelatoPlot |
| Run GENEPOP | genepop genepopWrite |
| 'gtypes' Class | gtypes gtypes-class |
| 'gtypes' Accessors | accessors getAlleleNames getAlleleNames,gtypes-method getDescription getDescription,gtypes-method getIndNames getIndNames,gtypes-method getLociNames getLociNames,gtypes-method getNumInd getNumInd,gtypes-method getNumLoci getNumLoci,gtypes-method getNumStrata getNumStrata,gtypes-method getOther getOther,gtypes-method getPloidy getPloidy,gtypes-method getSchemes getSchemes,gtypes-method getSequences getSequences,gtypes-method getStrata getStrata,gtypes-method getStrataNames getStrataNames,gtypes-method gtypes.accessors index setDescription setDescription<- setDescription<-,gtypes-method setOther setOther<- setOther<-,gtypes-method setSchemes setSchemes<- setSchemes<-,gtypes-method setStrata setStrata<- setStrata<-,gtypes-method subset [,gtypes,ANY,ANY,ANY-method |
| Convert Between 'gtypes' And 'genind' objects. | genind2gtypes gtypes2genind |
| Convert Between 'gtypes' And 'genlight' objects. | genlight2gtypes gtypes2genlight |
| Convert Between 'gtypes' And 'loci' objects. | gtypes2loci loci2gtypes |
| Convert Between 'gtypes' And 'phyDat' objects. | gtypes2phyDat phyDat2gtypes |
| Heterozygosity | heterozygosity |
| Hardy-Weinberg Equilibrium | HWE hwe hweTest |
| 'gtypes' Constructor | gtypes.initialize initialize,gtypes-method initialize.gtypes new |
| Test if object is 'gtypes' | is.gtypes |
| IUPAC Codes | iupac iupacCode iupacMat validIupacCodes |
| Find and label haplotypes | labelHaplotypes labelHaplotypes.character labelHaplotypes.default labelHaplotypes.gtypes labelHaplotypes.list |
| Convert Rmetasim landscape | landscape2df landscape2gtypes |
| Linkage Disequlibrium | LDgenepop |
| ldNe | ldNe |
| Low Frequency Substitutions | lowFreqSubs |
| Minor Allele Frequencies | maf |
| MAFFT Alignment | mafft |
| Run MavericK | maverickRun |
| Read and Write MEGA | MEGA mega mega, read.mega write.mega |
| Most Distant Sequences | mostDistantSequences |
| Representative Sequences | mostRepresentativeSequences |
| M ratio | mRatio |
| Dolphin Microsatellite gtypes Object | msats.g |
| Nei's Da | neiDa |
| Nucleotide Divergence | dA nucleotideDivergence |
| Nucleotide Diversity | nucleotideDiversity |
| Number of Alleles | numAlleles |
| Number of Individuals Genotyped | numGenotyped |
| Number Missing Data | numMissing |
| Permute strata | permuteStrata |
| PHASE | phase phaseFilter phasePosterior phaseReadPair phaseReadSample phaseWrite |
| Population Genetics Equations | expectedNumAlleles fstToNm numGensEq popGenEqns wrightFst |
| Population Structure Tests | overallTest pairwiseMatrix pairwiseSummary pairwiseTest popStructTest |
| Private Alleles | privateAlleles |
| Proportion Unique Alleles | propUniqueAlleles |
| Read Genetic Data | readGenData |
| Remove Unused Sequences | removeUnusedSequences |
| Convert Sequences To 'gtypes' | sequence2gtypes |
| Sequence Likelihoods | sequenceLikelihoods |
| Site Frequency Spectrum | sfs |
| Shared Loci | propSharedLoci sharedAlleles sharedLoci |
| Simulate Haplotypes | simGammaHaps |
| Split Strata | strataSplit |
| Stratify gtypes | stratify |
| STRUCTURE | structure structureRead structureRun structureWrite |
| Plot STRUCTURE Results | structurePlot |
| Summarize Genotypes and Sequences | summarizeAll |
| Individual Summaries | summarizeInds |
| Locus Summaries | summarizeLoci |
| Sequence Summaries | summarizeSeqs |
| Summarize gtypes Object | summary summary,gtypes-method summary.gtypes |
| Tajima's D | tajimasD |
| Theta | theta |
| Transition / Transversion Ratio | isTi isTv subType TiTvRatio |
| Trim N's From Sequences | trimNs |
| Variable Sites | variableSites |
| Write NEXUS File for SNAPP | write.nexus.snapp |
| Write 'gtypes' | writeGtypes |
