Summaries and Population Structure Analyses of Genetic Data


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Documentation for package ‘strataG’ version 2.4.905

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

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

-- A --

accessors 'gtypes' Accessors
alleleFreqs Allele Frequencies
alleleSplit Split Alleles For Diploid Data
allelicRichness Allelic Richness
arlequin Read and Write Arlequin Files
arlequinRead Read and Write Arlequin Files
arlequinWrite Read and Write Arlequin Files
arp2gtypes Read and Write Arlequin Files
as.data.frame Convert 'gtypes' to data.frame or matrix
as.data.frame-method Convert 'gtypes' to data.frame or matrix
as.data.frame.gtypes Convert 'gtypes' to data.frame or matrix
as.matrix Convert 'gtypes' to data.frame or matrix
as.matrix-method Convert 'gtypes' to data.frame or matrix
as.matrix.gtypes Convert 'gtypes' to data.frame or 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
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
expandHaplotypes Expand Haplotypes
expectedNumAlleles Population Genetics Equations

-- F --

fasta Read and Write FASTA
fixedDifferences Fixed Differences
fixedSites Fixed Sites
freq2GenData Convert Haplotype Frequency Matrices
fsc.input Input functions for fastsimcoal parameters
fscBlock_dna Input functions for fastsimcoal parameters
fscBlock_freq Input functions for fastsimcoal parameters
fscBlock_microsat Input functions for fastsimcoal parameters
fscBlock_snp Input functions for fastsimcoal parameters
fscBlock_standard Input functions for fastsimcoal parameters
fscCleanup Run fastsimcoal
fscDeme Input functions for fastsimcoal parameters
fscEstParam Input functions for fastsimcoal parameters
fscEvent Input functions for fastsimcoal parameters
fscRead Read fastsimcoal output
fscReadArp Read fastsimcoal output
fscReadParamEst Read fastsimcoal output
fscReadSFS Read fastsimcoal output
fscRun Run fastsimcoal
fscSettings Input functions for fastsimcoal parameters
fscSettingsDef Input functions for fastsimcoal parameters
fscSettingsDemes Input functions for fastsimcoal parameters
fscSettingsEst Input functions for fastsimcoal parameters
fscSettingsEvents Input functions for fastsimcoal parameters
fscSettingsGenetics Input functions for fastsimcoal parameters
fscSettingsMigration Input functions for fastsimcoal parameters
fscTutorial Run fastsimcoal
fscWrite Write fastsimcoal2 input files
fstToNm Population Genetics Equations
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.
getAlleleNames 'gtypes' Accessors
getAlleleNames-method 'gtypes' Accessors
getDescription 'gtypes' Accessors
getDescription-method 'gtypes' Accessors
getIndNames 'gtypes' Accessors
getIndNames-method 'gtypes' Accessors
getLociNames 'gtypes' Accessors
getLociNames-method 'gtypes' Accessors
getNumInd 'gtypes' Accessors
getNumInd-method 'gtypes' Accessors
getNumLoci 'gtypes' Accessors
getNumLoci-method 'gtypes' Accessors
getNumStrata 'gtypes' Accessors
getNumStrata-method 'gtypes' Accessors
getOther 'gtypes' Accessors
getOther-method 'gtypes' Accessors
getPloidy 'gtypes' Accessors
getPloidy-method 'gtypes' Accessors
getSchemes 'gtypes' Accessors
getSchemes-method 'gtypes' Accessors
getSequences 'gtypes' Accessors
getSequences-method 'gtypes' Accessors
getStrata 'gtypes' Accessors
getStrata-method 'gtypes' Accessors
getStrataNames 'gtypes' Accessors
getStrataNames-method 'gtypes' Accessors
gtypes 'gtypes' Class
gtypes-class 'gtypes' Class
gtypes.accessors 'gtypes' Accessors
gtypes.initialize 'gtypes' Constructor
gtypes2genind Convert Between 'gtypes' And 'genind' objects.
gtypes2loci Convert Between 'gtypes' And 'loci' objects.
gtypes2phyDat Convert Between 'gtypes' And 'phyDat' objects.

-- H --

heterozygosity Heterozygosity
Hstats Population structure statistics
HWE Hardy-Weinberg Equilibrium
hwe Hardy-Weinberg Equilibrium
hweTest Hardy-Weinberg Equilibrium

-- I --

index '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
iupac IUPAC Codes
iupacCode IUPAC Codes
iupacMat IUPAC Codes

-- L --

labelHaplotypes Find and label haplotypes
labelHaplotypes.character Find and label haplotypes
labelHaplotypes.default Find and label haplotypes
labelHaplotypes.gtypes Find and label haplotypes
labelHaplotypes.list Find and label haplotypes
landscape2df Convert Rmetasim landscape
landscape2gtypes Convert Rmetasim landscape
LDgenepop Linkage Disequlibrium
ldNe ldNe
loci2gtypes Convert Between 'gtypes' And 'loci' objects.
lowFreqSubs Low Frequency Substitutions

-- M --

maf Minor Allele Frequencies
mafft MAFFT Alignment
maverickRun Run MavericK
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
nucleotideDivergence Nucleotide Divergence
nucleotideDiversity Nucleotide Diversity
numAlleles Number of Alleles
numGenotyped Number of Individuals Genotyped
numGensEq Population Genetics Equations
numMissing Number Missing Data

-- O --

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.
popGenEqns Population Genetics Equations
popStructStat Population structure statistics
popStructTest Population Differentiation Tests
privateAlleles Private Alleles
propSharedLoci Shared Loci
propUniqueAlleles Proportion Unique Alleles

-- R --

read.arlequin Read and Write Arlequin Files
read.fasta Read and Write FASTA
read.mega Read and Write MEGA
readGenData Read Genetic Data
removeSequences Remove Sequences

-- S --

sequence2gtypes Convert Sequences To 'gtypes'
sequenceLikelihoods Sequence Likelihoods
setDescription 'gtypes' Accessors
setDescription<- 'gtypes' Accessors
setDescription<--method 'gtypes' Accessors
setOther 'gtypes' Accessors
setOther<- 'gtypes' Accessors
setOther<--method 'gtypes' Accessors
setSchemes 'gtypes' Accessors
setSchemes<- 'gtypes' Accessors
setSchemes<--method 'gtypes' Accessors
setStrata 'gtypes' Accessors
setStrata<- 'gtypes' Accessors
setStrata<--method 'gtypes' Accessors
sfs Site Frequency Spectrum
sharedAlleles Shared Loci
sharedLoci Shared Loci
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
statPhist Population structure statistics
strataG Summaries and population structure analyses of DNA sequence genotypic data
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
summarizeAll Summarize Genotypes and Sequences
summarizeInds Individual Summaries
summarizeLoci Locus Summaries
summarizeSeqs Sequence Summaries
summary Summarize gtypes Object
summary-method Summarize gtypes Object
summary.gtypes Summarize gtypes Object

-- T --

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

-- V --

validIupacCodes IUPAC Codes
variableSites Variable Sites

-- W --

wrightFst Population Genetics Equations
write.arlequin Read and Write Arlequin Files
write.fasta Read and Write FASTA
write.mega Read and Write MEGA
write.nexus.snapp Write NEXUS File for SNAPP
writeGtypes Write 'gtypes'

-- misc --

[-method 'gtypes' Accessors