Man pages for EricArcher/strataG
Summaries and Population Structure Analyses of Genetic Data

alleleFreqFormatCompiles and Formats Allele Frequencies
alleleFreqsAllele Frequencies
alleleSplitSplit Alleles For Diploid Data
allelicRichnessAllelic Richness
arlequinRead and Write Arlequin Files
as.array.gtypesConvert 'gtypes' To 'array'
as.data.frame.gtypesConvert 'gtypes' To 'data.frame'
as.matrix-gtypes-methodConvert 'gtypes' To 'matrix'
as.multidnaConvert to multidna
baseFreqsBase Frequencies
bowhead.snp.positionBowhead Whale SNP Genotype Groups
bowhead.snpsBowhead Whale SNP Genotypes
clumppRun CLUMPP
createConsensusConsensus Sequence
df2gtypesConvert a data.frame to gtypes
dloop.gDolphin dLoop gtypes Object
dolph.hapsDolphin mtDNA Haplotype Sequences
dolph.msatsDolphin Microsatellite Genotypes
dolph.seqsDolphin mtDNA D-loop Sequences
dolph.strataDolphin Genetic Stratification and Haplotypes
dupGenotypesDuplicate Genotypes
evannoRun Evanno Method on STRUCTURE Results
expandHaplotypesExpand haplotypes
fastaRead and Write FASTA
fastsimcoalRun fastsimcoal
fastsimcoal.inputInput functions for fastsimcoal parameters
fixedDifferencesFixed Differences
fixedSitesFixed Sites
freq2GenDataConvert Haplotype Frequency Matrices
fusFsFu's Fs
gelatoGELATo - Group ExcLusion and Assignment Test
genepopRun GENEPOP
gtypes2genindConvert Between 'gtypes' And 'genind' objects.
gtypes2lociConvert Between 'gtypes' And 'loci' objects.
gtypes2phyDatConvert Between 'gtypes' And 'phyDat' objects.
gtypes.accessors'gtypes' Accessors
gtypes-class'gtypes' Class
heterozygosityObserved and Expected Heterozygosity
hweTestHardy-Weinberg Equilibrium
initialize-gtypes-method'gtypes' Constructor
is.gtypesTest if object is 'gtypes'
iupacCodeIUPAC Code
jackHWEHardy-Weinberg Equlibrium Jackknife
labelHaplotypesFind and label haplotypes
LDgenepopLinkage Disequlibrium
ldNeldNe
lowFreqSubsLow Frequency Substitutions
mafMinimum Allele Frequencies
mafftMAFFT Alignment
maverickRunRun MavericK
megaRead and Write MEGA
mostDistantSequencesMost Distant Sequences
mostRepresentativeSequencesRepresentative Sequences
mRatioM ratio
msats.gDolphin Microsatellite gtypes Object
neiDaNei's Da
nucleotideDivergenceNucleotide Divergence
nucleotideDiversityNucleotide Diversity
numAllelesNumber of Alleles
numericSNPmatCreate a numeric SNP matrix
numGenotypedNumber of Individuals Genotyped
numMissingNumber Missing Data
permuteStrataPermute strata
phasePHASE
popGenEqnsPopulation Genetics Equations
popStructStatPopulation structure statistics
popStructTestPopulation Differentiation Tests
privateAllelesPrivate Alleles
propUniqueAllelesProportion Unique Alleles
qaqcQuality Assurance/Quality Control
readGenDataRead Genetic Data
removeSequencesRemove Sequences
sequence2gtypesConvert Sequences To 'gtypes'
sequenceLikelihoodsSequence Likelihoods
sharedLociShared Loci
show-gtypes-methodShow a gtypes object
simGammaHapsSimulate Haplotypes
strataG-internalInternal Functions
strataG-packageSummaries and population structure analyses of DNA sequence...
strataGUIstrataG GUI
strataSplitSplit Strata
stratifyStratify gtypes
structureSTRUCTURE
structurePlotPlot STRUCTURE Results
summarizeLociLocus Summaries
summarizeSamplesSample Summaries
summarizeSeqsSequence Summaries
summary-gtypes-methodSummarize gtypes Object
tajimasDTajima's D
thetaTheta
TiTvRatioTransition / Transversion Ratio
trimNsTrim N's From Sequences
validIupacCodesValid IUPAC Codes
variableSitesVariable Sites
write.gtypesWrite 'gtypes'
write.nexus.snappWrite NEXUS File for SNAPP
EricArcher/strataG documentation built on July 31, 2017, 11:17 p.m.