strataG: Summaries and Population Structure Analyses of Genetic Data

A toolkit for analyzing stratified population genetic data.

AuthorEric Archer [aut, cre], Paula Adams [aut], Brita Schneiders [aut]
Date of publication2016-12-05 18:28:48
MaintainerEric Archer <eric.archer@noaa.gov>
LicenseGNU General Public License
Version1.0.5

View on CRAN

Man pages

alleleFreqFormat: Compiles and Formats Allele Frequencies

alleleFreqs: Allele Frequencies

alleleSplit: Split Alleles For Diploid Data

allelicRichness: Allelic Richness

as.data.frame.gtypes: Convert 'gtypes' To 'data.frame'

as.matrix-gtypes-method: Convert 'gtypes' To 'matrix'

as.multidna: Convert to multidna

baseFreqs: Base Frequencies

bowhead.snp.position: Bowhead Whale SNP Genotype Groups

bowhead.snps: Bowhead Whale SNP Genotypes

clumpp: Run CLUMPP

createConsensus: Consensus Sequence

df2gtypes: Convert a data.frame to gtypes

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

dupGenotypes: Duplicate Genotypes

evanno: Run Evanno Method on STRUCTURE Results

expectedNumAlleles: Expected Number of Alleles

fasta: Read and Write FASTA

fastsimcoal: Run fastsimcoal

fastsimcoal.input: Input functions for fastsimcoal parameters

fixedDifferences: Fixed Differences

fixedSites: Fixed Sites

freq2GenData: Convert Haplotype Frequency Matrices

fstToNm: Nm from Fst

fusFs: Fu's Fs

gelato: GELATo - Group ExcLusion and Assignment Test

genepop: Run GENEPOP

gtypes2genind: Convert Between 'gtypes' And 'genind' objects.

gtypes2loci: Convert Between 'gtypes' And 'loci' objects.

gtypes2phyDat: Convert Between 'gtypes' And 'phyDat' objects.

gtypes.accessors: 'gtypes' Accessors

gtypes-class: 'gtypes' Class

haplotypeLikelihoods: Haplotype Likelihoods

heterozygosity: Observed and Expected Heterozygosity

hweTest: Hardy-Weinberg Equilibrium

idRows: 'gtypes' ID Rows

initialize-gtypes-method: 'gtypes' Constructor

is.gtypes: Test if object is 'gtypes'

iupacCode: IUPAC Code

jackHWE: Hardy-Weinberg Equlibrium Jackknife

labelHaplotypes: Find and label haplotypes

LDgenepop: Linkage Disequlibrium

lowFreqSubs: Low Frequency Substitutions

mafft: MAFFT Alignment

mega: Read and Write MEGA

mostDistantSequences: Most Distant Sequences

mostRepresentativeSequences: Representative Sequences

mRatio: M ratio

msats.g: Dolphin Microsatellite gtypes Object

neiDa: Nei's Da

nucleotideDivergence: Nucleotide Divergence

nucleotideDiversity: Nucleotide Diversity

numAlleles: Number of Alleles

numGensEq: Number of Generations to Equilibrium

numMissing: Number Missing Data

permuteStrata: Permute strata

phase: PHASE

popStructStat: Population structure statistics

popStructTest: Population Differentiation Tests

privateAlleles: Private Alleles

propUniqueAlleles: Proportion Unique Alleles

qaqc: Quality Assurance/Quality Control

readGenData: Read Genetic Data

removeSequences: Remove Sequences

sequence2gtypes: Convert Sequences To 'gtypes'

sharedLoci: Shared Loci

show-gtypes-method: Show a gtypes object

simGammaHaps: Simulate Haplotypes

strataG-internal: Internal Functions

strataG-package: Summaries and population structure analyses of DNA sequence...

strataSplit: Split Strata

stratify: Stratify gtypes

structure: STRUCTURE

structurePlot: Plot STRUCTURE Results

summarizeLoci: Locus Summaries

summarizeSeqs: Sequence Summaries

summary-gtypes-method: Summarize gtypes Object

tajimasD: Tajima's D

theta: Theta

TiTvRatio: Transition / Transversion Ratio

trimNs: Trim N's From Sequences

validIupacCodes: Valid IUPAC Codes

variableSites: Variable Sites

wrightFst: Wright's Fst

write.arlequin: Write Arlequin Input Files

write.gtypes: Write 'gtypes'

write.nexus.snapp: Write NEXUS File for SNAPP

Files in this package

strataG
strataG/inst
strataG/inst/extdata
strataG/inst/extdata/dolph.seqs.fasta
strataG/inst/doc
strataG/inst/doc/population.structure.R
strataG/inst/doc/population.structure.html
strataG/inst/doc/gtypes.Rmd
strataG/inst/doc/qaqc.Rmd
strataG/inst/doc/sequences.Rmd
strataG/inst/doc/summaries.R
strataG/inst/doc/qaqc.html
strataG/inst/doc/external.programs.Rmd
strataG/inst/doc/gtypes.html
strataG/inst/doc/sequences.R
strataG/inst/doc/gtypes.R
strataG/inst/doc/qaqc.R
strataG/inst/doc/summaries.html
strataG/inst/doc/population.structure.Rmd
strataG/inst/doc/external.programs.html
strataG/inst/doc/summaries.Rmd
strataG/inst/doc/sequences.html
strataG/src
strataG/src/statFis_C.cpp
strataG/src/statGst_C.cpp
strataG/src/statFst_C.cpp
strataG/src/statPhist_C.cpp
strataG/src/misc.funcs.cpp
strataG/src/Hstats_C.cpp
strataG/src/RcppExports.cpp
strataG/src/statChi2_C.cpp
strataG/src/statJostD_C.cpp
strataG/NAMESPACE
strataG/data
strataG/data/dolph.haps.rda
strataG/data/dolph.seqs.rda
strataG/data/dolph.strata.rda
strataG/data/bowhead.snps.rda
strataG/data/dolph.msats.rda
strataG/data/dloop.g.rda
strataG/data/msats.g.rda
strataG/data/bowhead.snp.position.rda
strataG/R
strataG/R/mega.R strataG/R/baseFreqs.R strataG/R/permuteStrata.R strataG/R/mRatio.R strataG/R/write.arlequin.R strataG/R/statJostD.R strataG/R/hweTest.R strataG/R/is.gtypes.R strataG/R/fstToNm.R strataG/R/numGensEq.R strataG/R/nucleotideDivergence.R strataG/R/structure.R strataG/R/Hstats.R strataG/R/gtypes2phyDat.R strataG/R/as.multidna.R strataG/R/trimNs.R strataG/R/stratify.R strataG/R/validIupacCodes.R strataG/R/sharedLoci.R strataG/R/readGenData.R strataG/R/LDgenepop.R strataG/R/labelHaplotypes.R strataG/R/fixedDifferences.R strataG/R/statFis.R strataG/R/strataG-internal.R strataG/R/numMissing.R strataG/R/evanno.R strataG/R/gtypes.class.R
strataG/R/sysdata.rda
strataG/R/haplotypeLikelihoods.R strataG/R/summarizeSeqs.R strataG/R/show.gtypes.R strataG/R/alleleFreqFormat.R strataG/R/iupacCode.R strataG/R/statChi2.R strataG/R/dupGenotypes.R strataG/R/write.nexus.snapp.R strataG/R/as.data.frame.gtypes.R strataG/R/gtypes2loci.R strataG/R/freq2GenData.R strataG/R/write.gtypes.R strataG/R/popStructStat.R strataG/R/lowFreqSubs.R strataG/R/expectedNumAlleles.R strataG/R/allelicRichness.R strataG/R/clumpp.R strataG/R/phase.R strataG/R/theta.R strataG/R/fixedSites.R strataG/R/gtypes2genind.R strataG/R/nucleotideDiversity.R strataG/R/jackHWE.R strataG/R/wrightFst.R strataG/R/RcppExports.R strataG/R/structurePlot.R strataG/R/fastsimcoal.input.R strataG/R/summarizeLoci.R strataG/R/variableSites.R strataG/R/summary.gtypes.R strataG/R/alleleFreqs.R strataG/R/statPhist.R strataG/R/mafft.R strataG/R/qaqc.R strataG/R/mostRepresentativeSequences.R strataG/R/df2gtypes.R strataG/R/mostDistantSequences.R strataG/R/initialize.gtypes.R strataG/R/fusFs.R strataG/R/idRows.R strataG/R/popStructTest.R strataG/R/statFst.R strataG/R/createConsensus.R strataG/R/tajimasD.R strataG/R/sequence2gtypes.R strataG/R/simGammaHaps.R strataG/R/removeSequences.R strataG/R/privateAlleles.R strataG/R/heterozygosity.R strataG/R/gelato.R strataG/R/genepop.R strataG/R/fastsimcoal.R strataG/R/fasta.R strataG/R/as.matrix.gtypes.R strataG/R/numAlleles.R strataG/R/strataG-package.R strataG/R/gtypes.accessors.R strataG/R/strataSplit.R strataG/R/alleleSplit.R strataG/R/propUniqueAlleles.R strataG/R/neiDa.R strataG/R/statGst.R strataG/R/TiTvRatio.R
strataG/vignettes
strataG/vignettes/gtypes.Rmd
strataG/vignettes/msats.csv
strataG/vignettes/qaqc.Rmd
strataG/vignettes/sequences.Rmd
strataG/vignettes/external.programs.Rmd
strataG/vignettes/population.structure.Rmd
strataG/vignettes/summaries.Rmd
strataG/README.md
strataG/MD5
strataG/build
strataG/build/vignette.rds
strataG/DESCRIPTION
strataG/man
strataG/man/removeSequences.Rd strataG/man/fastsimcoal.input.Rd strataG/man/dolph.seqs.Rd strataG/man/jackHWE.Rd strataG/man/strataG-package.Rd strataG/man/privateAlleles.Rd strataG/man/validIupacCodes.Rd strataG/man/is.gtypes.Rd strataG/man/write.arlequin.Rd strataG/man/qaqc.Rd strataG/man/lowFreqSubs.Rd strataG/man/variableSites.Rd strataG/man/hweTest.Rd strataG/man/allelicRichness.Rd strataG/man/numAlleles.Rd strataG/man/strataSplit.Rd strataG/man/nucleotideDiversity.Rd strataG/man/structure.Rd strataG/man/write.nexus.snapp.Rd strataG/man/freq2GenData.Rd strataG/man/haplotypeLikelihoods.Rd strataG/man/gtypes2loci.Rd strataG/man/fasta.Rd strataG/man/dolph.haps.Rd strataG/man/mega.Rd strataG/man/df2gtypes.Rd strataG/man/strataG-internal.Rd strataG/man/fixedSites.Rd strataG/man/popStructTest.Rd strataG/man/alleleSplit.Rd strataG/man/fusFs.Rd strataG/man/idRows.Rd strataG/man/iupacCode.Rd strataG/man/theta.Rd strataG/man/neiDa.Rd strataG/man/baseFreqs.Rd strataG/man/stratify.Rd strataG/man/simGammaHaps.Rd strataG/man/alleleFreqFormat.Rd strataG/man/initialize-gtypes-method.Rd strataG/man/gtypes2genind.Rd strataG/man/as.matrix-gtypes-method.Rd strataG/man/trimNs.Rd strataG/man/gtypes2phyDat.Rd strataG/man/show-gtypes-method.Rd strataG/man/fastsimcoal.Rd strataG/man/numMissing.Rd strataG/man/dolph.msats.Rd strataG/man/evanno.Rd strataG/man/tajimasD.Rd strataG/man/sequence2gtypes.Rd strataG/man/as.multidna.Rd strataG/man/write.gtypes.Rd strataG/man/fixedDifferences.Rd strataG/man/summary-gtypes-method.Rd strataG/man/mRatio.Rd strataG/man/structurePlot.Rd strataG/man/nucleotideDivergence.Rd strataG/man/createConsensus.Rd strataG/man/wrightFst.Rd strataG/man/gtypes.accessors.Rd strataG/man/TiTvRatio.Rd strataG/man/dolph.strata.Rd strataG/man/gtypes-class.Rd strataG/man/permuteStrata.Rd strataG/man/summarizeSeqs.Rd strataG/man/mostRepresentativeSequences.Rd strataG/man/labelHaplotypes.Rd strataG/man/dupGenotypes.Rd strataG/man/LDgenepop.Rd strataG/man/propUniqueAlleles.Rd strataG/man/alleleFreqs.Rd strataG/man/fstToNm.Rd strataG/man/summarizeLoci.Rd strataG/man/bowhead.snps.Rd strataG/man/genepop.Rd strataG/man/dloop.g.Rd strataG/man/expectedNumAlleles.Rd strataG/man/clumpp.Rd strataG/man/heterozygosity.Rd strataG/man/sharedLoci.Rd strataG/man/mafft.Rd strataG/man/as.data.frame.gtypes.Rd strataG/man/msats.g.Rd strataG/man/mostDistantSequences.Rd strataG/man/popStructStat.Rd strataG/man/phase.Rd strataG/man/readGenData.Rd strataG/man/gelato.Rd strataG/man/bowhead.snp.position.Rd strataG/man/numGensEq.Rd

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