Summaries and Population Structure Analyses of Genetic Data


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Documentation for package ‘strataG’ version 2.0.2

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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
arlequin Read and Write Arlequin Files
as.array Convert 'gtypes' To 'array'
as.array-method Convert 'gtypes' To 'array'
as.array.gtypes Convert 'gtypes' To 'array'
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
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
expandHaplotypes Expand haplotypes
expectedNumAlleles Population Genetics Equations
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 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.
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 --

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

-- I --

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

-- M --

maf Minimum 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
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
numericSNPmat Create a numeric SNP matrix
numGenotyped Number of Individuals Genotyped
numGensEq Population Genetics Equations
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
popGenEqns Population Genetics Equations
popStructStat Population structure statistics
popStructTest Population Differentiation Tests
print.gtypeSummary Summarize gtypes Object
privateAlleles Private Alleles
propUniqueAlleles Proportion Unique Alleles

-- Q --

qaqc Quality Assurance/Quality Control

-- 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 --

schemes 'gtypes' Accessors
schemes-method 'gtypes' Accessors
schemes<- 'gtypes' Accessors
schemes<--method 'gtypes' Accessors
sequence2gtypes Convert Sequences To 'gtypes'
sequenceLikelihoods Sequence Likelihoods
sequences 'gtypes' Accessors
sequences-method 'gtypes' Accessors
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
strataGUI strataG GUI
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
summarizeSamples Sample 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 Valid IUPAC Codes
variableSites Variable Sites

-- W --

wrightFst Population Genetics Equations
write.arlequin Read and Write Arlequin Files
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