podkat: Position-Dependent Kernel Association Test
Version 1.8.0

This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

AuthorUlrich Bodenhofer
Bioconductor views Annotation DataImport Genetics Sequencing VariantAnnotation WholeGenome
Date of publicationNone
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2)
Version1.8.0
URL http://www.bioinf.jku.at/software/podkat/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("podkat")

Getting started

Package overview

Popular man pages

assocTest-methods: Perform Association Test
hgA: Artificial Human Chromosome for Testing Purposes
partitionRegions-methods: Partition Genomic Regions
podkat-package: PODKAT Package
print-methods: Print Association Test Results
readRegionsFromBedFile: Read Genomic Regions from BED File
split-methods: Split 'GRanges' Object
See all...

All man pages Function index File listing

Man pages

assocTest-methods: Perform Association Test
AssocTestResult-class: Class 'AssocTestResult'
AssocTestResultRanges-class: Class 'AssocTestResultRanges'
computeKernel: Compute Kernel Matrix
filterResult-methods: Filter Association Test Results According to p-Values or...
GenotypeMatrix-class: Class 'GenotypeMatrix'
genotypeMatrix-methods: Constructors for Creating 'GenotypeMatrix' Objects
hgA: Artificial Human Chromosome for Testing Purposes
NullModel-class: Class 'NullModel'
nullModel-methods: Create Null Model for Association Test
p.adjust-methods: Adjust p-Value for Multiple Tests
partitionRegions-methods: Partition Genomic Regions
plot-methods: Plotting functions
podkat-package: PODKAT Package
print-methods: Print Association Test Results
qqplot-methods: Quantile-Quantile Plots
readGenotypeMatrix-methods: Read from VCF File
readRegionsFromBedFile: Read Genomic Regions from BED File
readSampleNamesFromVcfHeader: Read Sample Names from VCF File Header
readVariantInfo-methods: Read information about variants from VCF file
sort-methods: Sort Association Test Results
split-methods: Split 'GRanges' Object
unmasked-datasets: Unmasked Regions of Human Genomes
unmaskedRegions: Extract Unmasked Regions from 'MaskedBSgenome' Object
VariantInfo-class: Class 'VariantInfo'
weightFuncs: Weighting Functions
weights-methods: Extract Contribution Weights of Variants

Functions

AssocTestResult Man page
AssocTestResult-class Man page
AssocTestResultRanges Man page
AssocTestResultRanges-class Man page
GenotypeMatrix Man page
GenotypeMatrix-class Man page
MAF Man page
MAF,GenotypeMatrix-method Man page
MAF,VariantInfo-method Man page
NullModel Man page
NullModel-class Man page
VariantInfo Man page
VariantInfo-class Man page
[,GenotypeMatrix,index,index,missing-method Man page
[,GenotypeMatrix,index,missing,missing-method Man page
[,GenotypeMatrix,missing,index,missing-method Man page
[,NullModel,index,missing,missing-method Man page
assocTest Man page
assocTest,GenotypeMatrix,NullModel-method Man page
assocTest,TabixFile,NullModel-method Man page
assocTest,character,NullModel-method Man page
assocTest,matrix,NullModel-method Man page
assocTest-methods Man page
assocTest.GenotypeMatrix Source code
assocTest.TabixFile Source code
assocTest.TabixFileWorker Source code
assocTest.dgCMatrix Source code
assocTest.filename Source code
assocTest.kernelMatrix Source code
assocTest.linkernel Source code
b36Unmasked Man page
b37Unmasked Man page
betaWeights Man page Source code
c,AssocTestResultRanges-method Man page
c.AssocTestResultRanges Source code
check.arg.integer Source code
check.arg.logical Source code
check.arg.numeric Source code
class:AssocTestResult Man page
class:AssocTestResultRanges Man page
class:GenotypeMatrix Man page
class:NullModel Man page
class:VariantInfo Man page
coefficients,NullModel-method Man page
computeChiSquareParamsPopulation Source code
computeChiSquareParamsSKAT Source code
computeChiSquareParamsSample Source code
computeChiSquareParamsUnbiased Source code
computeKernel Man page Source code
computePvalues Source code
computePvaluesAdj Source code
computeWeights Source code
filterResult Man page
filterResult,AssocTestResultRanges-method Man page
filterResult,GRanges-method Man page
filterResult,GRangesList-method Man page
filterResult-methods Man page
filterResult.AssocTestResultRanges Source code
filterResult.GRanges Source code
genotypeMatrix Man page
genotypeMatrix,ANY,GRanges,missing-method Man page
genotypeMatrix,ANY,character,missing-method Man page
genotypeMatrix,ANY,missing,missing-method Man page
genotypeMatrix,ANY,numeric,character-method Man page
genotypeMatrix,eSet,character,character-method Man page
genotypeMatrix,eSet,character,missing-method Man page
genotypeMatrix,eSet,numeric,character-method Man page
genotypeMatrix-methods Man page
genotypeMatrix.ANY Source code
genotypeMatrix.Cmatrix.GRanges Source code
genotypeMatrix.dgCMatrix.GRanges Source code
hg18Unmasked Man page
hg19Unmasked Man page
hg38Unmasked Man page
hgA Man page
invSdWeights Man page Source code
length,NullModel-method Man page
logisticWeights Man page Source code
method:genotypeMatrix Man page
method:readGenotypeMatrix Man page
method:readVariantInfo Man page
names,NullModel-method Man page
nullModel Man page
nullModel,formula,data.frame-method Man page
nullModel,formula,missing-method Man page
nullModel,matrix,factor-method Man page
nullModel,matrix,numeric-method Man page
nullModel,missing,factor-method Man page
nullModel,missing,numeric-method Man page
nullModel-methods Man page
nullModel.X.y Source code
nullModel.formula Source code
nullModel.y Source code
p.adjust Man page
p.adjust,AssocTestResultRanges-method Man page
p.adjust-methods Man page
p.adjust.AssocTestResultRanges Source code
partitionRegions Man page
partitionRegions,GRanges-method Man page
partitionRegions,GRangesList-method Man page
partitionRegions,MaskedBSgenome-method Man page
partitionRegions-methods Man page
partitionRegions.GRanges Source code
plot Man page
plot,AssocTestResultRanges,GRanges-method Man page
plot,AssocTestResultRanges,character-method Man page
plot,AssocTestResultRanges,missing-method Man page
plot,GRanges,character-method Man page
plot,GenotypeMatrix,factor-method Man page
plot,GenotypeMatrix,missing-method Man page
plot,GenotypeMatrix,numeric-method Man page
plot-methods Man page
plot.AssocTestResultRanges.GRanges Source code
plot.AssocTestResultRanges.character Source code
plot.GRanges.character Source code
plot.GenotypeMatrix.factor Source code
plot.GenotypeMatrix.missing Source code
plot.GenotypeMatrix.numeric Source code
podkat Man page
podkat-package Man page
print Man page
print,AssocTestResultRanges-method Man page
print-methods Man page
print.AssocTestResultRanges Source code
qqplot Man page
qqplot,AssocTestResultRanges,AssocTestResultRanges-method Man page
qqplot,AssocTestResultRanges,missing-method Man page
qqplot-methods Man page
qqplot.AssocTestResultRanges Source code
qqplot.vector Source code
readGenotypeMatrix Man page
readGenotypeMatrix,TabixFile,GRanges-method Man page
readGenotypeMatrix,TabixFile,missing-method Man page
readGenotypeMatrix,character,GRanges-method Man page
readGenotypeMatrix,character,missing-method Man page
readGenotypeMatrix-methods Man page
readGenotypeMatrix.TabixFile Source code
readRegionsFromBedFile Man page Source code
readSampleNamesFromVcfHeader Man page Source code
readVariantInfo Man page
readVariantInfo,TabixFile,GRanges-method Man page
readVariantInfo,TabixFile,missing-method Man page
readVariantInfo,character,GRanges-method Man page
readVariantInfo,character,missing-method Man page
readVariantInfo-methods Man page
readVariantInfo.TabixFile Source code
resampling Source code
residuals,NullModel-method Man page
show,AssocTestResult-method Man page
show,AssocTestResultRanges-method Man page
show,GenotypeMatrix-method Man page
show,NullModel-method Man page
show,VariantInfo-method Man page
sort Man page
sort,AssocTestResultRanges-method Man page
sort-methods Man page
split Man page
split,GRanges,GRangesList-method Man page
split-methods Man page
summary,VariantInfo-method Man page
summary.VariantInfo Source code
unmasked-datasets Man page
unmaskedRegions Man page Source code
variantInfo Man page
variantInfo,GRanges-method Man page
variantInfo,GenotypeMatrix-method Man page
variantInfo,missing-method Man page
vcfScan Source code
vcfScanVariantInfo Source code
weightFuncs Man page
weights Man page
weights,AssocTestResult-method Man page
weights,AssocTestResultRanges-method Man page
weights-methods Man page
weights.AssocTestResult Source code
weights.AssocTestResultRanges.GenotypeMatrix Source code
weights.AssocTestResultRanges.TabixFile Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/access-methods.R
R/assocTest-methods.R
R/c-methods.R
R/coerce-methods.R
R/computeKernel.R
R/computePvalues.R
R/computeWeights.R
R/filterResult-methods.R
R/genotypeMatrix-methods.R
R/inputChecks.R
R/nullModel-methods.R
R/p.adjust-methods.R
R/partitionRegions-methods.R
R/plot-methods.R
R/print-methods.R
R/qqplot-methods.R
R/readGenotypeMatrix-methods.R
R/readRegionsFromBedFile.R
R/readSampleNamesFromVcfHeader.R
R/readVariantInfo-methods.R
R/resampling.R
R/show-methods.R
R/sort-methods.R
R/split-methods.R
R/summary-methods.R
R/unmaskedRegions.R
R/weightFuncs.R
R/weights-methods.R
build
build/vignette.rds
data
data/b36Unmasked.RData
data/b37Unmasked.RData
data/hg18Unmasked.RData
data/hg19Unmasked.RData
data/hg38Unmasked.RData
data/hgA.RData
inst
inst/CITATION
inst/COPYRIGHT
inst/NEWS
inst/doc
inst/doc/podkat.R
inst/doc/podkat.Rnw
inst/doc/podkat.pdf
inst/examples
inst/examples/HBA.bed
inst/examples/example1.vcf.gz
inst/examples/example1.vcf.gz.tbi
inst/examples/example1lin.csv
inst/examples/example1log.csv
man
man/AssocTestResult-class.Rd
man/AssocTestResultRanges-class.Rd
man/GenotypeMatrix-class.Rd
man/NullModel-class.Rd
man/VariantInfo-class.Rd
man/assocTest-methods.Rd
man/computeKernel.Rd
man/filterResult-methods.Rd
man/genotypeMatrix-methods.Rd
man/hgA.Rd
man/nullModel-methods.Rd
man/p.adjust-methods.Rd
man/partitionRegions-methods.Rd
man/plot-methods.Rd
man/podkat-package.Rd
man/print-methods.Rd
man/qqplot-methods.Rd
man/readGenotypeMatrix-methods.Rd
man/readRegionsFromBedFile.Rd
man/readSampleNamesFromVcfHeader.Rd
man/readVariantInfo-methods.Rd
man/sort-methods.Rd
man/split-methods.Rd
man/unmasked-datasets.Rd
man/unmaskedRegions.Rd
man/weightFuncs.Rd
man/weights-methods.Rd
src
src/Makevars
src/Makevars.win
src/R_init_podkat.cpp
src/bernoulliExact.cpp
src/bernoulliExact.h
src/checkAndFixGenotype.cpp
src/checkAndFixGenotype.h
src/cumMax.cpp
src/cumMax.h
src/doubleMale.cpp
src/doubleMale.h
src/errCodes.h
src/kernels.cpp
src/kernels.h
src/pValues.cpp
src/pValues.h
src/partitionRegions.cpp
src/partitionRegions.h
src/qfc.cpp
src/qfc.h
src/readGenotypeMatrix.cpp
src/readGenotypeMatrix.h
src/readVariantInfo.cpp
src/readVariantInfo.h
vignettes
vignettes/JKU_EN_noName.pdf
vignettes/PODKAT_example.pdf
vignettes/PODKAT_workflow.pdf
vignettes/PosKernel.pdf
vignettes/SKAT_example.pdf
vignettes/betaWeights.pdf
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/invSdWeights.pdf
vignettes/logisticWeights.pdf
vignettes/podkat.Rnw
podkat documentation built on May 20, 2017, 9:14 p.m.

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

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

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