strataG: Summaries and Population Structure Analyses of Genetic Data

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A toolkit for analyzing stratified population genetic data.

Author
Eric Archer [aut, cre], Paula Adams [aut], Brita Schneiders [aut]
Date of publication
2016-12-05 18:28:48
Maintainer
Eric Archer <eric.archer@noaa.gov>
License
GNU General Public License
Version
1.0.5

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