strataG: Summaries and Population Structure Analyses of Genetic Data
Version 2.0.2

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) .

Browse man pages Browse package API and functions Browse package files

AuthorEric Archer [aut, cre], Paula Adams [aut], Brita Schneiders [aut], Sarina Fernandez [aut], Warren Asfazadour [aut]
Date of publication2017-04-11 11:00:39 UTC
MaintainerEric Archer <eric.archer@noaa.gov>
LicenseGNU General Public License
Version2.0.2
URL https://github.com/EricArcher/strataG
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("strataG")

Man pages

alleleFreqFormat: Compiles and Formats Allele Frequencies
alleleFreqs: Allele Frequencies
alleleSplit: Split Alleles For Diploid Data
allelicRichness: Allelic Richness
arlequin: Read and Write Arlequin Files
as.array.gtypes: Convert 'gtypes' To 'array'
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
expandHaplotypes: Expand haplotypes
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
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
heterozygosity: Observed and Expected Heterozygosity
hweTest: Hardy-Weinberg Equilibrium
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
ldNe: ldNe
lowFreqSubs: Low Frequency Substitutions
maf: Minimum Allele Frequencies
mafft: MAFFT Alignment
maverickRun: Run MavericK
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
numericSNPmat: Create a numeric SNP matrix
numGenotyped: Number of Individuals Genotyped
numMissing: Number Missing Data
permuteStrata: Permute strata
phase: PHASE
popGenEqns: Population Genetics Equations
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'
sequenceLikelihoods: Sequence Likelihoods
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...
strataGUI: strataG GUI
strataSplit: Split Strata
stratify: Stratify gtypes
structure: STRUCTURE
structurePlot: Plot STRUCTURE Results
summarizeLoci: Locus Summaries
summarizeSamples: Sample 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
write.gtypes: Write 'gtypes'
write.nexus.snapp: Write NEXUS File for SNAPP

Functions

.applyPerLocus Man page
.getFileLabel Man page
.numericLoci Man page
.parseLocusNames Man page
.propSharedIds Man page
.removeIdsMissingAllLoci Man page
.setupClusters Man page
.strataPairs Man page
HWE Man page
HoCalc Source code
HsCalc Source code
Hstats Man page Source code
Hstats_C Source code
LDgenepop Man page Source code
MEGA Man page
TiTvRatio Man page Source code
[,gtypes,ANY,ANY,ANY-method Man page
accessors Man page
alleleFreqFormat Man page Source code
alleleFreqs Man page Source code
alleleNames Man page Man page
alleleNames,gtypes-method Man page
alleleSplit Man page Source code
allelicRichness Man page Source code
applyPerLocus Source code
arlequin Man page
as.array Man page
as.array,gtypes-method Man page
as.array.gtypes Man page
as.data.frame Man page
as.data.frame,gtypes-method Man page
as.data.frame.gtypes Man page
as.matrix Man page
as.matrix,gtypes-method Man page
as.matrix.gtypes Man page
as.multidna Man page Source code
baseFreqs Man page Source code
baseSmry Source code
bowhead.snp.position Man page
bowhead.snps Man page
calcStrataN Source code
checkStrataMat Source code
clumpp Man page Source code
colMeanC Source code
colSumC Source code
createConsensus Man page Source code
dA Man page
description Man page Man page Man page
description,gtypes-method Man page
description<- Man page
description<-,gtypes-method Man page
df2gtypes Man page Source code
dloop.g Man page
dolph.haps Man page
dolph.msats Man page
dolph.seqs Man page
dolph.strata Man page
dupGenotypes Man page Source code
evanno Man page Source code
expandHaplotypes Man page Source code
expectedNumAlleles Man page Source code
exptdHet Man page Source code
fasta Man page
fastsimcoal Man page Man page Source code
fastsimcoal.input Man page
fixedDifferences Man page Source code
fixedSites Man page Source code
formatCinput Source code
formatResult Source code
freq2GenData Man page Source code
fscHistEv Man page Source code
fscLocusParams Man page Source code
fscPopInfo Man page Source code
fscRead Man page Source code
fscWrite Man page Source code
fstToNm Man page Source code
fusFs Man page Source code
gelato Man page Source code
gelatoPlot Man page Source code
genepop Man page Source code
genepopWrite Man page Source code
genind2gtypes Man page Source code
getFileLabel Source code
getMaxInt Source code
gtypes Man page
gtypes-class Man page
gtypes.accessors Man page
gtypes2genind Man page Source code
gtypes2loci Man page Source code
gtypes2phyDat Man page Source code
heterozygosity Man page
hwe Man page
hweTest Man page Source code
idGenotype Source code
idStart Source code
indNames Man page
indNames,gtypes-method Man page
index Man page
initialize,gtypes-method Man page
initialize.gtypes Man page
intOuterC Source code
is.gtypes Man page Source code
isTi Man page Source code
isTv Man page Source code
iupacCode Man page Source code
jackHWE Man page Source code
jackInfluential Man page Source code
labelHaplotypes Man page Source code
labelHaplotypes.character Man page Source code
labelHaplotypes.default Man page Source code
labelHaplotypes.gtypes Man page Source code
labelHaplotypes.list Man page Source code
ldNe Man page Source code
locNames Man page
locNames,gtypes-method Man page
loci2gtypes Man page Source code
lowFreqSubs Man page Source code
mRatio Man page Source code
maf Man page Source code
mafft Man page Source code
maverickDefaultParams Source code
maverickRun Man page Source code
mega Man page
mega, Man page
mostDistantSequences Man page Source code
mostRepresentativeSequences Man page Source code
msats.g Man page
nInd Man page
nInd,gtypes-method Man page
nLoc Man page
nLoc,gtypes-method Man page
nStrata Man page Man page
nStrata,gtypes-method Man page
neiDa Man page Source code
new Man page
nucleotideDivergence Man page Source code
nucleotideDiversity Man page Source code
numAlleles Man page Source code
numGenotyped Man page Source code
numGensEq Man page Source code
numMissing Man page Source code
numOuterC Source code
numericLoci Source code
numericSNPmat Man page Source code
obsvdHet Man page Source code
other Man page
other,gtypes-method Man page
overallTest Man page Source code
pairwiseTest Man page Source code
parseLocusNames Source code
permStrata Source code
permuteStrata Man page Source code
phase Man page Source code
phaseFilter Man page Source code
phasePosterior Man page Source code
phaseReadPair Man page Source code
phaseReadSample Man page Source code
phaseWrite Man page Source code
phyDat2gtypes Man page Source code
ploidy Man page
ploidy,gtypes-method Man page
plot.jack.influential Man page Source code
popGenEqns Man page
popStructStat Man page
popStructTest Man page Source code
print.gtypeSummary Man page Source code
printBaseSmry Source code
privateAlleles Man page Source code
propSharedIds Source code
propSharedLoci Man page Source code
propUniqueAlleles Man page Source code
qaqc Man page Source code
read.arlequin Man page Source code
read.fasta Man page Source code
read.mega Man page Source code
readGenData Man page Source code
removeIdsMissingAllLoci Source code
removeSequences Man page Source code
rowSumC Source code
schemes Man page Man page Man page
schemes,gtypes-method Man page
schemes<- Man page
schemes<-,gtypes-method Man page
sequence2gtypes Man page Source code
sequenceLikelihoods Man page Source code
sequences Man page Man page
sequences,gtypes-method Man page
setupClusters Source code
sharedAlleles Man page Source code
sharedLoci Man page
show,gtypes-method Man page
show.gtypes Man page
simGammaHaps Man page Source code
statChi2 Man page Source code
statChi2_C Source code
statFis Man page Source code
statFis_C Source code
statFst Man page Source code
statFstPrime Man page Source code
statFstPrime_C Source code
statFst_C Source code
statGst Man page Source code
statGstDblPrime Man page Source code
statGstDblPrime_C Source code
statGstPrime Man page Source code
statGstPrime_C Source code
statGst_C Source code
statJostD Man page Source code
statJostD_C Source code
statList Man page Source code
statPhist Man page Source code
statPhist_C Source code
strata Man page Man page
strata,gtypes-method Man page
strata<- Man page
strata<-,gtypes-method Man page
strataG Man page
strataG-internal Man page
strataG-package Man page
strataGUI Man page Source code
strataNames Man page Man page
strataNames,gtypes-method Man page
strataPairs Source code
strataSplit Man page Source code
stratify Man page Source code
structure Man page
structureParseQmat Source code
structurePlot Man page Source code
structureRead Man page Source code
structureRun Man page Source code
structureWrite Man page Source code
subType Man page Source code
subset Man page
summarizeLoci Man page Source code
summarizeSamples Man page Source code
summarizeSeqs Man page Source code
summary Man page
summary,gtypes-method Man page Man page
summary.gtypes Man page
table2D Source code
tajimasD Man page Source code
theta Man page Source code
trimNs Man page Source code
validIupacCodes Man page Source code
variableSites Man page Source code
wrightFst Man page Source code
write.arlequin Man page Source code
write.fasta Man page Source code
write.gtypes Man page Source code
write.mega Man page Source code
write.nexus.snapp Man page Source code

Files

inst
inst/CITATION
inst/shiny
inst/shiny/setup
inst/shiny/setup/ui.setup.R
inst/shiny/setup/server.setup.R
inst/shiny/load.data
inst/shiny/load.data/server.load.ui.sidepanel.rdata.R
inst/shiny/load.data/server.load.ui.sidepanel.csv.R
inst/shiny/load.data/server.load.display.gtypes.R
inst/shiny/load.data/server.load.ui.R
inst/shiny/load.data/server.load.R
inst/shiny/load.data/ui.load.R
inst/shiny/app.R
inst/shiny/popstruct
inst/shiny/popstruct/server.popstruct.ui.R
inst/shiny/popstruct/ui.popstruct.R
inst/shiny/popstruct/server.popstruct.R
inst/shiny/qaqc
inst/shiny/qaqc/ui.qaqc.haploid.R
inst/shiny/qaqc/server.qaqc.02.loci.hmzg.R
inst/shiny/qaqc/ui.qaqc.diploid.R
inst/shiny/qaqc/server.qaqc.03.samples.missing.R
inst/shiny/qaqc/server.qaqc.08.reports.R
inst/shiny/qaqc/server.qaqc.04.samples.hmzg.R
inst/shiny/qaqc/server.qaqc.haploid.R
inst/shiny/qaqc/ui.qaqc.R
inst/shiny/qaqc/server.qaqc.06.hwe.jack.R
inst/shiny/qaqc/server.qaqc.01.loci.missing.R
inst/shiny/qaqc/server.qaqc.R
inst/shiny/qaqc/server.qaqc.summaries.R
inst/shiny/qaqc/server.qaqc.05.dups.R
inst/shiny/qaqc/server.qaqc.07.ld.R
inst/shiny/global.R
inst/extdata
inst/extdata/dolph.seqs.fasta
inst/doc
inst/doc/population.structure.R
inst/doc/population.structure.html
inst/doc/gtypes.Rmd
inst/doc/qaqc.Rmd
inst/doc/sequences.Rmd
inst/doc/summaries.R
inst/doc/qaqc.html
inst/doc/external.programs.Rmd
inst/doc/gtypes.html
inst/doc/sequences.R
inst/doc/gtypes.R
inst/doc/qaqc.R
inst/doc/summaries.html
inst/doc/population.structure.Rmd
inst/doc/external.programs.html
inst/doc/summaries.Rmd
inst/doc/sequences.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test-popStructStats.R
src
src/statFis_C.cpp
src/statGst_C.cpp
src/statFst_C.cpp
src/statPhist_C.cpp
src/misc.funcs.cpp
src/Hstats_C.cpp
src/init.c
src/RcppExports.cpp
src/statChi2_C.cpp
src/statJostD_C.cpp
NAMESPACE
data
data/dolph.haps.rda
data/dolph.seqs.rda
data/dolph.strata.rda
data/bowhead.snps.rda
data/dolph.msats.rda
data/dloop.g.rda
data/msats.g.rda
data/bowhead.snp.position.rda
R
R/mega.R
R/baseFreqs.R
R/permuteStrata.R
R/mRatio.R
R/as.array.gtypes.R
R/summarizeSamples.R
R/hweTest.R
R/is.gtypes.R
R/nucleotideDivergence.R
R/structure.R
R/gtypes2phyDat.R
R/as.multidna.R
R/trimNs.R
R/stratify.R
R/validIupacCodes.R
R/sharedLoci.R
R/readGenData.R
R/LDgenepop.R
R/labelHaplotypes.R
R/numericSNPmat.R
R/fixedDifferences.R
R/strataG-internal.R
R/numMissing.R
R/evanno.R
R/gtypes.class.R
R/popGenEqns.R
R/sysdata.rda
R/summarizeSeqs.R
R/show.gtypes.R
R/alleleFreqFormat.R
R/iupacCode.R
R/maverickRun.R
R/dupGenotypes.R
R/write.nexus.snapp.R
R/as.data.frame.gtypes.R
R/gtypes2loci.R
R/freq2GenData.R
R/write.gtypes.R
R/popStructStat.R
R/lowFreqSubs.R
R/strataGUI.R
R/allelicRichness.R
R/arlequin.R
R/clumpp.R
R/phase.R
R/theta.R
R/fixedSites.R
R/gtypes2genind.R
R/expandHaplotypes.R
R/nucleotideDiversity.R
R/jackHWE.R
R/RcppExports.R
R/structurePlot.R
R/fastsimcoal.input.R
R/summarizeLoci.R
R/variableSites.R
R/ldNe.R
R/summary.gtypes.R
R/alleleFreqs.R
R/mafft.R
R/qaqc.R
R/mostRepresentativeSequences.R
R/df2gtypes.R
R/mostDistantSequences.R
R/initialize.gtypes.R
R/fusFs.R
R/popStructTest.R
R/createConsensus.R
R/numGenotyped.R
R/tajimasD.R
R/sequence2gtypes.R
R/simGammaHaps.R
R/removeSequences.R
R/privateAlleles.R
R/heterozygosity.R
R/sequenceLikelihoods.R
R/gelato.R
R/genepop.R
R/maf.R
R/fastsimcoal.R
R/fasta.R
R/as.matrix.gtypes.R
R/numAlleles.R
R/strataG-package.R
R/gtypes.accessors.R
R/strataSplit.R
R/alleleSplit.R
R/propUniqueAlleles.R
R/neiDa.R
R/TiTvRatio.R
vignettes
vignettes/gtypes.Rmd
vignettes/msats.csv
vignettes/qaqc.Rmd
vignettes/sequences.Rmd
vignettes/external.programs.Rmd
vignettes/population.structure.Rmd
vignettes/summaries.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/removeSequences.Rd
man/fastsimcoal.input.Rd
man/dolph.seqs.Rd
man/jackHWE.Rd
man/strataG-package.Rd
man/privateAlleles.Rd
man/validIupacCodes.Rd
man/is.gtypes.Rd
man/qaqc.Rd
man/popGenEqns.Rd
man/lowFreqSubs.Rd
man/variableSites.Rd
man/hweTest.Rd
man/allelicRichness.Rd
man/expandHaplotypes.Rd
man/numAlleles.Rd
man/strataSplit.Rd
man/nucleotideDiversity.Rd
man/maverickRun.Rd
man/structure.Rd
man/write.nexus.snapp.Rd
man/freq2GenData.Rd
man/gtypes2loci.Rd
man/fasta.Rd
man/dolph.haps.Rd
man/mega.Rd
man/ldNe.Rd
man/df2gtypes.Rd
man/strataGUI.Rd
man/numericSNPmat.Rd
man/maf.Rd
man/strataG-internal.Rd
man/fixedSites.Rd
man/popStructTest.Rd
man/alleleSplit.Rd
man/fusFs.Rd
man/numGenotyped.Rd
man/iupacCode.Rd
man/theta.Rd
man/neiDa.Rd
man/baseFreqs.Rd
man/sequenceLikelihoods.Rd
man/stratify.Rd
man/simGammaHaps.Rd
man/alleleFreqFormat.Rd
man/initialize-gtypes-method.Rd
man/summarizeSamples.Rd
man/gtypes2genind.Rd
man/as.array.gtypes.Rd
man/as.matrix-gtypes-method.Rd
man/trimNs.Rd
man/gtypes2phyDat.Rd
man/show-gtypes-method.Rd
man/fastsimcoal.Rd
man/numMissing.Rd
man/dolph.msats.Rd
man/evanno.Rd
man/tajimasD.Rd
man/sequence2gtypes.Rd
man/as.multidna.Rd
man/write.gtypes.Rd
man/fixedDifferences.Rd
man/summary-gtypes-method.Rd
man/mRatio.Rd
man/structurePlot.Rd
man/nucleotideDivergence.Rd
man/createConsensus.Rd
man/gtypes.accessors.Rd
man/arlequin.Rd
man/TiTvRatio.Rd
man/dolph.strata.Rd
man/gtypes-class.Rd
man/permuteStrata.Rd
man/summarizeSeqs.Rd
man/mostRepresentativeSequences.Rd
man/labelHaplotypes.Rd
man/dupGenotypes.Rd
man/LDgenepop.Rd
man/propUniqueAlleles.Rd
man/alleleFreqs.Rd
man/summarizeLoci.Rd
man/bowhead.snps.Rd
man/genepop.Rd
man/dloop.g.Rd
man/clumpp.Rd
man/heterozygosity.Rd
man/sharedLoci.Rd
man/mafft.Rd
man/as.data.frame.gtypes.Rd
man/msats.g.Rd
man/mostDistantSequences.Rd
man/popStructStat.Rd
man/phase.Rd
man/readGenData.Rd
man/gelato.Rd
man/bowhead.snp.position.Rd
strataG documentation built on May 19, 2017, 10:07 a.m.