SeqVarTools: Tools for variant data

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

Author
Stephanie M. Gogarten, Xiuwen Zheng, Adrienne Stilp
Date of publication
None
Maintainer
Stephanie M. Gogarten <sdmorris@u.washington.edu>, Xiuwen Zheng <zhengx@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
License
GPL-3
Version
1.12.0

View on Bioconductor

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

Files in this package

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