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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SeqVarTools")
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
Version1.12.0

View on Bioconductor

Functions

alleleDosage Man page
alleleDosage,SeqVarGDSClass,list-method Man page
alleleDosage,SeqVarGDSClass,numeric-method Man page
alleleFrequency Man page
alleleFrequency,SeqVarGDSClass-method Man page
allele-methods 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,character-method Man page
applyMethod,SeqVarGDSClass,function,GRanges-method Man page
applyMethod,SeqVarGDSClass,function,missing-method Man page
applyMethod,SeqVarGDSClass,function,numeric-method Man page
countSingletons Man page
countSingletons,SeqVarGDSClass-method Man page
duplicateDiscordance Man page
duplicateDiscordance,SeqVarData,missing-method Man page
duplicateDiscordance,SeqVarData,SeqVarData-method Man page
getGenotype Man page
getGenotypeAlleles Man page
getGenotypeAlleles,SeqVarGDSClass-method Man page
getGenotype,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
inbreedCoeff Man page
inbreedCoeff,SeqVarGDSClass-method Man page
isSNV Man page
isSNV,SeqVarGDSClass-method Man page
isVariant Man page
isVariant,SeqVarGDSClass-method Man page
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
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
refFracOverHets Man page
refFracOverHets,SeqVarGDSClass-method Man page
refFracPlot Man page
refFracPlot,SeqVarGDSClass-method Man page
refFrac,SeqVarGDSClass-method Man page
regression Man page
regression,SeqVarData-method Man page
sampleData Man page
sampleData<- Man page
sampleData<-,SeqVarData,AnnotatedDataFrame-method Man page
sampleData,SeqVarData-method Man page
SeqVarData Man page
SeqVarData-class Man page
SeqVarTools Man page
SeqVarTools-package Man page
setVariantID Man page
titv Man page
titv,SeqVarGDSClass-method Man page
variantData Man page
variantData<- Man page
variantData<-,SeqVarData,AnnotatedDataFrame-method Man page
variantData,SeqVarData-method Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.