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>.

Install the latest version of this package by entering the following in R:
install.packages("strataG")
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
https://github.com/EricArcher/strataG

View on CRAN

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

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

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

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