SeqVarTools: Tools for variant data
Version 1.14.0

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

AuthorStephanie M. Gogarten, Xiuwen Zheng, Adrienne Stilp
Bioconductor views GeneticVariability Genetics SNP Sequencing
Date of publicationNone
MaintainerStephanie M. Gogarten <sdmorris@u.washington.edu>, Xiuwen Zheng <zhengx@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
LicenseGPL-3
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SeqVarTools")

Getting started

Package overview
README.md

Popular man pages

allele-methods: Extract allele information from a GDS object
alternateAlleleDetection: alternateAlleleDetection
hwe: Exact test for Hardy-Weinberg equilibrium
pca: Principal Component Analysis
regression: Linear or logistic regression
SeqVarData-class: SeqVarData
titv: Transition/Transversion Ratio
See all...

All man pages Function index File listing

Man pages

alleleFrequency: Allele frequency
allele-methods: Extract allele information from a GDS object
alternateAlleleDetection: alternateAlleleDetection
applyMethod: Apply method to GDS object
countSingletons: Count singletons
duplicateDiscordance: Duplicate discordance
getGenotype: Get genotype data
getVariableLengthData: Get variable-length data
heterozygosity: Heterozygosity and Homozygosity
hwe: Exact test for Hardy-Weinberg equilibrium
inbreedCoeff: Inbreeding coefficient
isSNV: Flag single nucleotide variants
isVariant: Locate variant samples across sites
meanBySample: Mean value by sample
mendelErr: Mendelian errors
missingGenotypeRate: Missing genotype rate
pca: Principal Component Analysis
pedigree: Pedigree for example data
refFrac: Reference allele fraction
regression: Linear or logistic regression
SeqVarData-class: SeqVarData
SeqVarTools-package: Tools for Variant Analysis
setVariantID: Change the variant ID of a GDS file
titv: Transition/Transversion Ratio

Functions

SeqVarData Man page Source code
SeqVarData-class Man page
SeqVarTools Man page
SeqVarTools-package Man page
allele-methods Man page
alleleDosage Man page
alleleDosage,SeqVarGDSClass,list-method Man page
alleleDosage,SeqVarGDSClass,numeric-method Man page
alleleFrequency Man page
alleleFrequency,SeqVarGDSClass-method Man page
alleleMatch Source code
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 Source code
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
applyNames Source code
autosomeErr Source code
callType Source code
countGenotypes Source code
countSingletons Man page
countSingletons,SeqVarGDSClass-method Man page
duplicateDiscordance Man page
duplicateDiscordance,SeqVarData,SeqVarData-method Man page
duplicateDiscordance,SeqVarData,missing-method Man page
f Source code
falseNeg Source code
falsePos Source code
freqByOutcome Source code
freqFromBinary Source code
genoMatch Source code
getAlt Source code
getGRanges Source code
getGenotype Man page
getGenotype,SeqVarGDSClass-method Man page
getGenotypeAlleles Man page
getGenotypeAlleles,SeqVarGDSClass-method Man page
getGenotypeClass Source code
getMatchesAltConc Source code
getMatchesConc Source code
getMatchesHetAlt Source code
getMatchesHetHom Source code
getMatchesHetRef Source code
getMatchesRefAlt Source code
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
inbreedCoeff Man page
inbreedCoeff,SeqVarGDSClass-method Man page
isSNV Man page
isSNV,SeqVarGDSClass-method Man page
isVariant Man page
isVariant,SeqVarGDSClass-method Man page
matchSamples Source code
matchVariants Source code
maxAlleleLength Source code
meanBySample Man page
meanBySample,SeqVarGDSClass-method Man page
mendelErr Man page
mendelErr,SeqVarGDSClass-method Man page
missingGenotypeRate Man page
missingGenotypeRate,SeqVarGDSClass-method Man page
nAlleles Man page
nAlleles,SeqVarGDSClass-method Man page
nHetRef Source code
nHomAlt Source code
nHomRef Source code
nSamp Source code
nSampUnfiltered Source code
nVar Source code
nVarUnfiltered Source code
outputNames Source code
parseAltAllele Source code
parseNumAlleles Source code
parseRefAllele Source code
parseVariableLength Source code
pca Man page
pca,SeqVarGDSClass-method Man page
pedigree Man page
permuteGenotypes Source code
rangesToID Source code
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
runFirth Source code
runRegression Source code
sTransition Source code
sTransversion Source code
sampleData Man page
sampleData,SeqVarData-method Man page
sampleData<- Man page
sampleData<-,SeqVarData,AnnotatedDataFrame-method Man page
samplePairs Source code
setVariantID Man page Source code
titv Man page
titv,SeqVarGDSClass-method Man page
trioType Source code
triosFromPedigree Source code
trueNeg Source code
truePos Source code
varTitle Source code
variantData Man page
variantData,SeqVarData-method Man page
variantData<- Man page
variantData<-,SeqVarData,AnnotatedDataFrame-method Man page
waldTest Source code
xMaleErr Source code
yMaleErr Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/AllUtilities.R
R/Methods-SeqVarData.R
R/Methods-SeqVarGDSClass.R
R/alternateAlleleDetection.R
R/duplicateDiscordance.R
R/hwe.R
R/inbreedCoeff.R
R/mendelErr.R
R/pca.R
R/refFrac.R
R/regression.R
R/setVariantID.R
README.md
build
build/vignette.rds
data
data/pedigree.RData
inst
inst/NEWS.Rd
inst/doc
inst/doc/SeqVarTools.R
inst/doc/SeqVarTools.Rnw
inst/doc/SeqVarTools.pdf
inst/extdata
inst/extdata/gl_chr1.gds
inst/extdata/gl_chr1.vcf
inst/extdata/hapmap_annotation.txt
inst/extdata/hapmap_annotation_DD.txt
inst/extdata/hapmap_exome_chr22.gds
inst/unitTests
inst/unitTests/test_SeqVarData.R
inst/unitTests/test_VariableLength.R
inst/unitTests/test_alleleFrequency.R
inst/unitTests/test_alleles.R
inst/unitTests/test_alternateAlleleDetection.R
inst/unitTests/test_applyMethod.R
inst/unitTests/test_countSingletons.R
inst/unitTests/test_duplicateDiscordance.R
inst/unitTests/test_getData.R
inst/unitTests/test_hethom.R
inst/unitTests/test_hwe.R
inst/unitTests/test_inbreedCoeff.R
inst/unitTests/test_meanBySample.R
inst/unitTests/test_mendelErr.R
inst/unitTests/test_missingGenotypeRate.R
inst/unitTests/test_pca.R
inst/unitTests/test_refFrac.R
inst/unitTests/test_regression.R
inst/unitTests/test_setVariantID.R
inst/unitTests/test_titv.R
inst/unitTests/test_utils.R
man
man/SeqVarData-class.Rd
man/SeqVarTools-package.Rd
man/allele-methods.Rd
man/alleleFrequency.Rd
man/alternateAlleleDetection.Rd
man/applyMethod.Rd
man/countSingletons.Rd
man/duplicateDiscordance.Rd
man/getGenotype.Rd
man/getVariableLengthData.Rd
man/heterozygosity.Rd
man/hwe.Rd
man/inbreedCoeff.Rd
man/isSNV.Rd
man/isVariant.Rd
man/meanBySample.Rd
man/mendelErr.Rd
man/missingGenotypeRate.Rd
man/pca.Rd
man/pedigree.Rd
man/refFrac.Rd
man/regression.Rd
man/setVariantID.Rd
man/titv.Rd
tests
tests/test.R
vignettes
vignettes/SeqVarTools.Rnw
vignettes/SeqVarTools.bib
SeqVarTools documentation built on May 20, 2017, 10:18 p.m.

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