# Summaries and Population Structure Analyses of Genetic Data

## Documentation for package ‘strataG’ version 1.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I J L M N O P Q R S T V W misc

strataG-package | Summaries and population structure analyses of DNA sequence genotypic data

## -- A --

accessors | 'gtypes' Accessors
alleleFreqFormat | Compiles and Formats Allele Frequencies
alleleFreqs | Allele Frequencies
alleleNames | 'gtypes' Accessors
alleleNames-method | 'gtypes' Accessors
alleleSplit | Split Alleles For Diploid Data
allelicRichness | Allelic Richness
as.data.frame | Convert 'gtypes' To 'data.frame'
as.data.frame-method | Convert 'gtypes' To 'data.frame'
as.data.frame.gtypes | Convert 'gtypes' To 'data.frame'
as.matrix | Convert 'gtypes' To 'matrix'
as.matrix-method | Convert 'gtypes' To 'matrix'
as.matrix.gtypes | Convert 'gtypes' To 'matrix'
as.multidna | Convert to multidna

## -- B --

baseFreqs | Base Frequencies
bowhead.snp.position | Bowhead Whale SNP Genotype Groups
bowhead.snps | Bowhead Whale SNP Genotypes

## -- C --

clumpp | Run CLUMPP
createConsensus | Consensus Sequence

## -- D --

dA | Nucleotide Divergence
description | 'gtypes' Accessors
description-method | 'gtypes' Accessors
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

## -- E --

evanno | Run Evanno Method on STRUCTURE Results
expectedNumAlleles | Expected Number of Alleles
exptdHet | Observed and Expected Heterozygosity

## -- F --

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
fscHistEv | Input functions for fastsimcoal parameters
fscLocusParams | Input functions for fastsimcoal parameters
fscPopInfo | Input functions for fastsimcoal parameters
fscRead | Run fastsimcoal
fscWrite | Run fastsimcoal
fstToNm | Nm from Fst
fusFs | Fu's Fs

## -- G --

gelato | GELATo - Group ExcLusion and Assignment Test
gelatoPlot | GELATo - Group ExcLusion and Assignment Test
genepop | Run GENEPOP
genepopWrite | Run GENEPOP
genind2gtypes | Convert Between 'gtypes' And 'genind' objects.
gtypes | 'gtypes' Class
gtypes-class | 'gtypes' Class
gtypes.accessors | 'gtypes' Accessors
gtypes2genind | Convert Between 'gtypes' And 'genind' objects.
gtypes2loci | Convert Between 'gtypes' And 'loci' objects.
gtypes2phyDat | Convert Between 'gtypes' And 'phyDat' objects.

## -- H --

haplotypeLikelihoods | Haplotype Likelihoods
heterozygosity | Observed and Expected Heterozygosity
Hstats | Population structure statistics
HWE | Hardy-Weinberg Equilibrium
hwe | Hardy-Weinberg Equilibrium
hweTest | Hardy-Weinberg Equilibrium

## -- I --

idRows | 'gtypes' ID Rows
index | 'gtypes' Accessors
indNames | 'gtypes' Accessors
indNames-method | 'gtypes' Accessors
initialize-method | 'gtypes' Constructor
initialize.gtypes | 'gtypes' Constructor
is.gtypes | Test if object is 'gtypes'
isTi | Transition / Transversion Ratio
isTv | Transition / Transversion Ratio
iupacCode | IUPAC Code

## -- J --

jackHWE | Hardy-Weinberg Equlibrium Jackknife
jackInfluential | Hardy-Weinberg Equlibrium Jackknife

## -- L --

labelHaplotypes | Find and label haplotypes
labelHaplotypes.default | Find and label haplotypes
labelHaplotypes.gtypes | Find and label haplotypes
LDgenepop | Linkage Disequlibrium
loci | 'gtypes' Accessors
loci-method | 'gtypes' Accessors
loci2gtypes | Convert Between 'gtypes' And 'loci' objects.
locNames | 'gtypes' Accessors
locNames-method | 'gtypes' Accessors
lowFreqSubs | Low Frequency Substitutions

## -- M --

mafft | MAFFT Alignment
MEGA | Read and Write MEGA
mega | Read and Write MEGA
mega, | Read and Write MEGA
mostDistantSequences | Most Distant Sequences
mostRepresentativeSequences | Representative Sequences
mRatio | M ratio
msats.g | Dolphin Microsatellite gtypes Object

## -- N --

neiDa | Nei's Da
new | 'gtypes' Constructor
nInd | 'gtypes' Accessors
nInd-method | 'gtypes' Accessors
nLoc | 'gtypes' Accessors
nLoc-method | 'gtypes' Accessors
nStrata | 'gtypes' Accessors
nStrata-method | 'gtypes' Accessors
nucleotideDivergence | Nucleotide Divergence
nucleotideDiversity | Nucleotide Diversity
numAlleles | Number of Alleles
numGensEq | Number of Generations to Equilibrium
numMissing | Number Missing Data

## -- O --

obsvdHet | Observed and Expected Heterozygosity
other | 'gtypes' Accessors
other-method | 'gtypes' Accessors
overallTest | Population Differentiation Tests

## -- P --

pairwiseTest | Population Differentiation Tests
permuteStrata | Permute strata
phase | PHASE
phaseFilter | PHASE
phasePosterior | PHASE
phaseReadPair | PHASE
phaseReadSample | PHASE
phaseWrite | PHASE
phyDat2gtypes | Convert Between 'gtypes' And 'phyDat' objects.
ploidy | 'gtypes' Accessors
ploidy-method | 'gtypes' Accessors
plot.jack.influential | Hardy-Weinberg Equlibrium Jackknife
popStructStat | Population structure statistics
popStructTest | Population Differentiation Tests
print.gtypeSummary | Summarize gtypes Object
privateAlleles | Private Alleles
propSharedIds | Shared Loci
propSharedLoci | Shared Loci
propUniqueAlleles | Proportion Unique Alleles

## -- Q --

qaqc | Quality Assurance/Quality Control

## -- R --

read.fasta | Read and Write FASTA
read.mega | Read and Write MEGA
readGenData | Read Genetic Data
removeSequences | Remove Sequences

## -- S --

schemes | 'gtypes' Accessors
schemes-method | 'gtypes' Accessors
schemes<- | 'gtypes' Accessors
schemes<--method | 'gtypes' Accessors
sequence2gtypes | Convert Sequences To 'gtypes'
sequences | 'gtypes' Accessors
sequences-method | 'gtypes' Accessors
sharedAlleles | Shared Loci
sharedLoci | Shared Loci
show-method | Show a gtypes object
show.gtypes | Show a gtypes object
simGammaHaps | Simulate Haplotypes
statChi2 | Population structure statistics
statFis | Population structure statistics
statFst | Population structure statistics
statFstPrime | Population structure statistics
statGst | Population structure statistics
statGstDblPrime | Population structure statistics
statGstPrime | Population structure statistics
statJostD | Population structure statistics
statList | Population Differentiation Tests
statPhist | Population structure statistics
strata | 'gtypes' Accessors
strata-method | 'gtypes' Accessors
strata<- | 'gtypes' Accessors
strata<--method | 'gtypes' Accessors
strataG | Summaries and population structure analyses of DNA sequence genotypic data
strataNames | 'gtypes' Accessors
strataNames-method | 'gtypes' Accessors
strataSplit | Split Strata
stratify | Stratify gtypes
structure | STRUCTURE
structurePlot | Plot STRUCTURE Results
structureRead | STRUCTURE
structureRun | STRUCTURE
structureWrite | STRUCTURE
subset | 'gtypes' Accessors
subType | Transition / Transversion Ratio
summarizeLoci | Locus Summaries
summarizeSeqs | Sequence Summaries
summary | Summarize gtypes Object
summary-method | Summarize gtypes Object

## -- T --

tajimasD | Tajima's D
theta | Theta
TiTvRatio | Transition / Transversion Ratio
trimNs | Trim N's From Sequences

## -- V --

validIupacCodes | Valid IUPAC Codes
variableSites | Variable Sites

## -- W --

wrightFst | Wright's Fst
write.fasta | Read and Write FASTA
write.gtypes | Write 'gtypes'
write.mega | Read and Write MEGA
write.nexus.snapp | Write NEXUS File for SNAPP

## -- misc --

[-method | 'gtypes' Accessors