SeqVarTools
Tools for variant data

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Functions
211
Source code
44
Man pages
28
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SeqVarTools: Tools for variant data
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API

API for SeqVarTools
Tools for variant data

Global functions
.alleleCount Source code
.alleleMatch Source code
.applyMethod Source code
.applyNames Source code
.autosomeErr Source code
.callType Source code
.countGenotypes Source code
.emptyDim Source code
.emptyGenoMatrix Source code
.emptySampFilter Source code
.emptyVarFilter Source code
.f Source code
.falseNeg Source code
.falsePos Source code
.freqByOutcome Source code
.freqFromBinary Source code
.genoMatch Source code
.getAlt Source code
.getGRanges Source code
.getGenotypeClass Source code
.getMatchesAltConc Source code
.getMatchesConc Source code
.getMatchesHetAlt Source code
.getMatchesHetHom Source code
.getMatchesHetRef Source code
.getMatchesRefAlt Source code
.getNonMissing Source code
.isTransition Source code
.isTransversion Source code
.matchSamples Source code
.matchVariants Source code
.maxAlleleLength Source code
.nHetRef Source code
.nHomAlt Source code
.nHomRef Source code
.nSamp Source code
.nSampObserved Source code
.nSampUnfiltered Source code
.nVar Source code
.nVarUnfiltered Source code
.outputNames Source code
.parseAltAllele Source code
.parseRefAllele Source code
.parseVariableLength Source code
.permuteGenotypes Source code
.ploidy Source code
.rangesToID Source code
.rangesToSel Source code
.runFirth Source code
.runRegression Source code
.samplePairs Source code
.samplePairs1 Source code
.subjectByQuery Source code
.subsetByUniqueOverlaps Source code
.testData Source code
.testDosageData Source code
.testSeqVarData Source code
.trioType Source code
.triosFromPedigree Source code
.trueNeg Source code
.truePos Source code
.varTitle Source code
.waldTest Source code
.xMaleErr Source code
.yMaleErr Source code
SeqVarBlockIterator Man page Source code
SeqVarBlockIterator-class Man page
SeqVarData Man page Source code
SeqVarData-class Man page
SeqVarIterator Man page Source code
SeqVarIterator-class Man page
SeqVarListIterator Man page Source code
SeqVarListIterator-class Man page
SeqVarRangeIterator Man page Source code
SeqVarRangeIterator-class Man page
SeqVarTools Man page
SeqVarTools-package Man page
SeqVarWindowIterator Man page Source code
SeqVarWindowIterator-class Man page
allele-methods Man page
alleleCount Man page
alleleCount,SeqVarData-method Man page
alleleCount,SeqVarGDSClass-method Man page
alleleDosage Man page
alleleDosage,SeqVarGDSClass,list-method Man page
alleleDosage,SeqVarGDSClass,numeric-method Man page
alleleFrequency Man page
alleleFrequency,SeqVarData-method Man page
alleleFrequency,SeqVarGDSClass-method Man page
altChar Man page
altChar,SeqVarGDSClass-method Man page
altDosage Man page
altDosage,SeqVarGDSClass-method Man page
alternateAlleleDetection Man page
alternateAlleleDetection,SeqVarData,SeqVarData-method Man page
applyMethod Man page
applyMethod,SeqVarGDSClass,function,GRanges-method Man page
applyMethod,SeqVarGDSClass,function,character-method Man page
applyMethod,SeqVarGDSClass,function,missing-method Man page
applyMethod,SeqVarGDSClass,function,numeric-method Man page
chromWithPAR Man page
chromWithPAR,SeqVarGDSClass-method Man page
countSingletons Man page
countSingletons,SeqVarGDSClass-method Man page
currentRanges Man page
currentRanges,SeqVarBlockIterator-method Man page
currentRanges,SeqVarListIterator-method Man page
currentRanges,SeqVarRangeIterator-method Man page
currentVariants Man page
currentVariants,SeqVarBlockIterator-method Man page
currentVariants,SeqVarIterator-method Man page
duplicateDiscordance Man page
duplicateDiscordance,SeqVarData,SeqVarData-method Man page
duplicateDiscordance,SeqVarData,missing-method Man page
duplicateDiscordance,SeqVarIterator,missing-method Man page
duplicateDiscordance1 Source code
expandedAltDosage Man page
expandedAltDosage,SeqVarGDSClass-method Man page
expandedVariantIndex Man page
expandedVariantIndex,SeqVarGDSClass-method Man page
getGenotype Man page
getGenotype,SeqVarGDSClass-method Man page
getGenotypeAlleles Man page
getGenotypeAlleles,SeqVarGDSClass-method Man page
getVariableLengthData Man page
getVariableLengthData,SeqVarGDSClass,character-method Man page
granges Man page
granges,SeqVarData-method Man page
heterozygosity Man page
heterozygosity,SeqVarGDSClass-method Man page
hethom Man page
hethom,SeqVarGDSClass-method Man page
homozygosity Man page
homozygosity,SeqVarGDSClass-method Man page
hwe Man page
hwe,SeqVarGDSClass-method Man page
imputedDosage Man page
imputedDosage,SeqVarGDSClass-method Man page
inbreedCoeff Man page
inbreedCoeff,SeqVarGDSClass-method Man page
isSNV Man page
isSNV,SeqVarGDSClass-method Man page
isVariant Man page
isVariant,SeqVarGDSClass-method Man page
iterateFilter Man page
iterateFilter,SeqVarIterator-method Man page
lastFilter Man page
lastFilter,SeqVarIterator-method Man page
lastFilter<- Man page
lastFilter<-,SeqVarIterator,numeric-method Man page
meanBySample Man page
meanBySample,SeqVarGDSClass-method Man page
mendelErr Man page
mendelErr,SeqVarGDSClass-method Man page
minorAlleleCount Man page
minorAlleleCount,SeqVarData-method Man page
minorAlleleCount,SeqVarGDSClass-method Man page
missingGenotypeRate Man page
missingGenotypeRate,SeqVarGDSClass-method Man page
nAlleles Man page
nAlleles,SeqVarGDSClass-method Man page
pca Man page
pca,SeqVarGDSClass-method Man page
pedigree Man page
refChar Man page
refChar,SeqVarGDSClass-method Man page
refDosage Man page
refDosage,SeqVarGDSClass-method Man page
refFrac Man page
refFrac,SeqVarGDSClass-method Man page
refFracOverHets Man page
refFracOverHets,SeqVarGDSClass-method Man page
refFracPlot Man page
refFracPlot,SeqVarGDSClass-method Man page
regression Man page
regression,SeqVarData-method Man page
resetIterator Man page
resetIterator,SeqVarIterator-method Man page
sampleData Man page
sampleData,SeqVarData-method Man page
sampleData<- Man page
sampleData<-,SeqVarData,AnnotatedDataFrame-method Man page
setVariantID Man page Source code
show,SeqVarData-method Man page
show,SeqVarIterator-method Man page
show,SeqVarListIterator-method Man page
show,SeqVarRangeIterator-method Man page
titv Man page
titv,SeqVarGDSClass-method Man page
validateSex Man page
validateSex,SeqVarData-method Man page
variantBlock Man page
variantBlock,SeqVarBlockIterator-method Man page
variantData Man page
variantData,SeqVarData-method Man page
variantData<- Man page
variantData<-,SeqVarData,AnnotatedDataFrame-method Man page
variantFilter Man page
variantFilter,SeqVarIterator-method Man page
variantInfo Man page
variantInfo,SeqVarGDSClass-method Man page
variantRanges Man page
variantRanges,SeqVarListIterator-method Man page
variantRanges,SeqVarRangeIterator-method Man page
SeqVarTools documentation built on Nov. 22, 2020, 2 a.m.

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