Package: SeqVarTools 1.43.0

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'))

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

Datasets:

pedigree - Pedigree for example data

On BioConductor:SeqVarTools-1.43.0(bioc 3.20)SeqVarTools-1.42.0(bioc 3.19)

bioconductor-package

60 exports 2.09 score 86 dependencies 2 dependents 4 mentions

Last updated 2 months agofrom:dbb2b6c7b5

Exports:alleleCount alleleDosage alleleFrequency altChar altDosage alternateAlleleDetection applyMethod chromWithPAR countSingletons currentRanges currentVariants duplicateDiscordance expandedAltDosage expandedVariantIndex getGenotype getGenotypeAlleles getVariableLengthData granges heterozygosity hethom homozygosity hwe imputedDosage inbreedCoeff isSNV isVariant iterateFilter lastFilter lastFilter<-meanBySample mendelErr minorAlleleCount missingGenotypeRate nAlleles pca refChar refDosage refFrac refFracOverHets refFracPlot regression resetIterator sampleData sampleData<-SeqVarBlockIterator SeqVarData SeqVarIterator SeqVarListIterator SeqVarRangeIterator SeqVarWindowIterator setVariantID show titv validateSex variantBlock variantData variantData<-variantFilter variantInfo variantRanges

Dependencies:askpass backports Biobase BiocGenerics Biostrings bit bit64 boot broom cli clipr codetools cpp11 crayon curl data.table dplyr fansi forcats foreach formula.tools gdsfmt generics GenomeInfoDb GenomeInfoDbData GenomicRanges glmnet glue GWASExactHW haven hms httr IRanges iterators jomo jsonlite lattice lifecycle lme4 logistf magrittr MASS Matrix mgcv mice mime minqa mitml nlme nloptr nnet numDeriv openssl operator.tools ordinal pan pillar pkgconfig prettyunits progress purrr R6 Rcpp RcppEigen readr rlang rpart S4Vectors SeqArray shape stringi stringr survival sys tibble tidyr tidyselect tzdb ucminf UCSC.utils utf8 vctrs vroom withr XVector zlibbioc

Introduction to SeqVarTools

Rendered fromSeqVarTools.Rnwusingutils::Sweaveon Jul 03 2024.

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

Iterators in SeqVarTools

Rendered fromIterators.Rnwusingutils::Sweaveon Jul 03 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for Variant Analysis	SeqVarTools-package SeqVarTools
Extract allele information from a GDS object	allele-methods altChar altChar,SeqVarGDSClass-method nAlleles nAlleles,SeqVarGDSClass-method refChar refChar,SeqVarGDSClass-method
Allele frequency	alleleCount alleleCount,SeqVarData-method alleleCount,SeqVarGDSClass-method alleleFrequency alleleFrequency,SeqVarData-method alleleFrequency,SeqVarGDSClass-method minorAlleleCount minorAlleleCount,SeqVarData-method minorAlleleCount,SeqVarGDSClass-method
alternateAlleleDetection	alternateAlleleDetection alternateAlleleDetection,SeqVarData,SeqVarData-method
Apply method to GDS object	applyMethod applyMethod,SeqVarGDSClass,function,character-method applyMethod,SeqVarGDSClass,function,GRanges-method applyMethod,SeqVarGDSClass,function,missing-method applyMethod,SeqVarGDSClass,function,numeric-method
Identify pseudoautosomal region	chromWithPAR chromWithPAR,SeqVarGDSClass-method
Count singletons	countSingletons countSingletons,SeqVarGDSClass-method
Duplicate discordance	duplicateDiscordance duplicateDiscordance,SeqVarData,missing-method duplicateDiscordance,SeqVarData,SeqVarData-method duplicateDiscordance,SeqVarIterator,missing-method
Get genotype data	alleleDosage 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 data	getVariableLengthData getVariableLengthData,SeqVarGDSClass,character-method
Heterozygosity and Homozygosity	heterozygosity heterozygosity,SeqVarGDSClass-method hethom hethom,SeqVarGDSClass-method homozygosity homozygosity,SeqVarGDSClass-method
Exact test for Hardy-Weinberg equilibrium	hwe hwe,SeqVarGDSClass-method
Get imputed dosage	imputedDosage imputedDosage,SeqVarGDSClass-method
Inbreeding coefficient	inbreedCoeff inbreedCoeff,SeqVarGDSClass-method
Flag single nucleotide variants	isSNV isSNV,SeqVarGDSClass-method
Locate variant samples across sites	isVariant isVariant,SeqVarGDSClass-method
Iterators	currentRanges 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 sample	meanBySample meanBySample,SeqVarGDSClass-method
Mendelian errors	mendelErr mendelErr,SeqVarGDSClass-method
Missing genotype rate	missingGenotypeRate missingGenotypeRate,SeqVarGDSClass-method
Principal Component Analysis	pca pca,SeqVarGDSClass-method
Pedigree for example data	pedigree
Reference allele fraction	refFrac refFrac,SeqVarGDSClass-method refFracOverHets refFracOverHets,SeqVarGDSClass-method refFracPlot refFracPlot,SeqVarGDSClass-method
Linear or logistic regression	regression regression,SeqVarData-method
SeqVarData	granges 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 file	setVariantID
Transition/Transversion Ratio	titv titv,SeqVarGDSClass-method
Variant info	expandedVariantIndex expandedVariantIndex,SeqVarGDSClass-method variantInfo variantInfo,SeqVarGDSClass-method