Package: SeqVarTools 1.45.0

Stephanie M. Gogarten

SeqVarTools: Tools for variant data

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

Authors:Stephanie M. Gogarten, Xiuwen Zheng, Adrienne Stilp

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SeqVarTools.pdf |SeqVarTools.html✨
SeqVarTools/json (API)
NEWS

# Install 'SeqVarTools' in R:
install.packages('SeqVarTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/smgogarten/seqvartools/issues

Datasets:

On BioConductor:SeqVarTools-1.45.0(bioc 3.21)SeqVarTools-1.44.0(bioc 3.20)

snpgeneticvariabilitysequencinggenetics

8.76 score 3 stars 2 packages 384 scripts 763 downloads 4 mentions 60 exports 86 dependencies

Last updated 2 months agofrom:6162bf608b. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winOKDec 19 2024
R-4.4-macOKDec 19 2024
R-4.3-winOKDec 19 2024
R-4.3-macOKDec 19 2024

Exports:alleleCountalleleDosagealleleFrequencyaltCharaltDosagealternateAlleleDetectionapplyMethodchromWithPARcountSingletonscurrentRangescurrentVariantsduplicateDiscordanceexpandedAltDosageexpandedVariantIndexgetGenotypegetGenotypeAllelesgetVariableLengthDatagrangesheterozygosityhethomhomozygosityhweimputedDosageinbreedCoeffisSNVisVariantiterateFilterlastFilterlastFilter<-meanBySamplemendelErrminorAlleleCountmissingGenotypeRatenAllelespcarefCharrefDosagerefFracrefFracOverHetsrefFracPlotregressionresetIteratorsampleDatasampleData<-SeqVarBlockIteratorSeqVarDataSeqVarIteratorSeqVarListIteratorSeqVarRangeIteratorSeqVarWindowIteratorsetVariantIDshowtitvvalidateSexvariantBlockvariantDatavariantData<-variantFiltervariantInfovariantRanges

Dependencies:askpassbackportsBiobaseBiocGenericsBiostringsbitbit64bootbroomclicliprcodetoolscpp11crayoncurldata.tabledplyrfansiforcatsforeachformula.toolsgdsfmtgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglmnetglueGWASExactHWhavenhmshttrIRangesiteratorsjomojsonlitelatticelifecyclelme4logistfmagrittrMASSMatrixmgcvmicemimeminqamitmlnlmenloptrnnetnumDerivopenssloperator.toolsordinalpanpillarpkgconfigprettyunitsprogresspurrrR6RcppRcppEigenreadrrlangrpartS4VectorsSeqArrayshapestringistringrsurvivalsystibbletidyrtidyselecttzdbucminfUCSC.utilsutf8vctrsvroomwithrXVectorzlibbioc

Introduction to SeqVarTools

Rendered fromSeqVarTools.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2017-08-23
Started: 2013-08-26

Iterators in SeqVarTools

Rendered fromIterators.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2019-04-12
Started: 2019-04-12

Readme and manuals

Help Manual

Help pageTopics
Tools for Variant AnalysisSeqVarTools-package SeqVarTools
Extract allele information from a GDS objectallele-methods altChar altChar,SeqVarGDSClass-method nAlleles nAlleles,SeqVarGDSClass-method refChar refChar,SeqVarGDSClass-method
Allele frequencyalleleCount alleleCount,SeqVarData-method alleleCount,SeqVarGDSClass-method alleleFrequency alleleFrequency,SeqVarData-method alleleFrequency,SeqVarGDSClass-method minorAlleleCount minorAlleleCount,SeqVarData-method minorAlleleCount,SeqVarGDSClass-method
alternateAlleleDetectionalternateAlleleDetection alternateAlleleDetection,SeqVarData,SeqVarData-method
Apply method to GDS objectapplyMethod applyMethod,SeqVarGDSClass,function,character-method applyMethod,SeqVarGDSClass,function,GRanges-method applyMethod,SeqVarGDSClass,function,missing-method applyMethod,SeqVarGDSClass,function,numeric-method
Identify pseudoautosomal regionchromWithPAR chromWithPAR,SeqVarGDSClass-method
Count singletonscountSingletons countSingletons,SeqVarGDSClass-method
Duplicate discordanceduplicateDiscordance duplicateDiscordance,SeqVarData,missing-method duplicateDiscordance,SeqVarData,SeqVarData-method duplicateDiscordance,SeqVarIterator,missing-method
Get genotype dataalleleDosage alleleDosage,SeqVarGDSClass,list-method alleleDosage,SeqVarGDSClass,numeric-method altDosage altDosage,SeqVarGDSClass-method expandedAltDosage expandedAltDosage,SeqVarGDSClass-method getGenotype getGenotype,SeqVarGDSClass-method getGenotypeAlleles getGenotypeAlleles,SeqVarGDSClass-method refDosage refDosage,SeqVarGDSClass-method
Get variable-length datagetVariableLengthData getVariableLengthData,SeqVarGDSClass,character-method
Heterozygosity and Homozygosityheterozygosity heterozygosity,SeqVarGDSClass-method hethom hethom,SeqVarGDSClass-method homozygosity homozygosity,SeqVarGDSClass-method
Exact test for Hardy-Weinberg equilibriumhwe hwe,SeqVarGDSClass-method
Get imputed dosageimputedDosage imputedDosage,SeqVarGDSClass-method
Inbreeding coefficientinbreedCoeff inbreedCoeff,SeqVarGDSClass-method
Flag single nucleotide variantsisSNV isSNV,SeqVarGDSClass-method
Locate variant samples across sitesisVariant isVariant,SeqVarGDSClass-method
IteratorscurrentRanges currentRanges,SeqVarBlockIterator-method currentRanges,SeqVarListIterator-method currentRanges,SeqVarRangeIterator-method currentVariants currentVariants,SeqVarBlockIterator-method currentVariants,SeqVarIterator-method iterateFilter iterateFilter,SeqVarIterator-method lastFilter lastFilter,SeqVarIterator-method lastFilter<- lastFilter<-,SeqVarIterator,numeric-method resetIterator resetIterator,SeqVarIterator-method SeqVarBlockIterator SeqVarBlockIterator-class SeqVarIterator SeqVarIterator-class SeqVarListIterator SeqVarListIterator-class SeqVarRangeIterator SeqVarRangeIterator-class SeqVarWindowIterator SeqVarWindowIterator-class show,SeqVarIterator-method show,SeqVarListIterator-method show,SeqVarRangeIterator-method variantBlock variantBlock,SeqVarBlockIterator-method variantFilter variantFilter,SeqVarIterator-method variantRanges variantRanges,SeqVarListIterator-method variantRanges,SeqVarRangeIterator-method
Mean value by samplemeanBySample meanBySample,SeqVarGDSClass-method
Mendelian errorsmendelErr mendelErr,SeqVarGDSClass-method
Missing genotype ratemissingGenotypeRate missingGenotypeRate,SeqVarGDSClass-method
Principal Component Analysispca pca,SeqVarGDSClass-method
Pedigree for example datapedigree
Reference allele fractionrefFrac refFrac,SeqVarGDSClass-method refFracOverHets refFracOverHets,SeqVarGDSClass-method refFracPlot refFracPlot,SeqVarGDSClass-method
Linear or logistic regressionregression regression,SeqVarData-method
SeqVarDatagranges granges,SeqVarData-method sampleData sampleData,SeqVarData-method sampleData<- sampleData<-,SeqVarData,AnnotatedDataFrame-method SeqVarData SeqVarData-class show,SeqVarData-method validateSex validateSex,SeqVarData-method variantData variantData,SeqVarData-method variantData<- variantData<-,SeqVarData,AnnotatedDataFrame-method
Change the variant ID of a GDS filesetVariantID
Transition/Transversion Ratiotitv titv,SeqVarGDSClass-method
Variant infoexpandedVariantIndex expandedVariantIndex,SeqVarGDSClass-method variantInfo variantInfo,SeqVarGDSClass-method