podkat: Position-Dependent Kernel Association Test

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("podkat")
AuthorUlrich Bodenhofer
Bioconductor views Annotation DataImport Genetics Sequencing VariantAnnotation WholeGenome
Date of publicationNone
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2)
Version1.6.1
http://www.bioinf.jku.at/software/podkat/

View on Bioconductor

Functions

assocTest Man page
assocTest,character,NullModel-method Man page
assocTest,GenotypeMatrix,NullModel-method Man page
assocTest,matrix,NullModel-method Man page
assocTest-methods Man page
AssocTestResult Man page
AssocTestResult-class Man page
AssocTestResultRanges Man page
AssocTestResultRanges-class Man page
assocTest,TabixFile,NullModel-method Man page
b36Unmasked Man page
b37Unmasked Man page
betaWeights Man page
c,AssocTestResultRanges-method Man page
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
computeKernel Man page
filterResult Man page
filterResult,AssocTestResultRanges-method Man page
filterResult,GRangesList-method Man page
filterResult,GRanges-method Man page
filterResult-methods Man page
genotypeMatrix Man page
GenotypeMatrix Man page
genotypeMatrix,ANY,character,missing-method Man page
genotypeMatrix,ANY,GRanges,missing-method Man page
genotypeMatrix,ANY,missing,missing-method Man page
genotypeMatrix,ANY,numeric,character-method Man page
GenotypeMatrix-class Man page
genotypeMatrix,eSet,character,character-method Man page
genotypeMatrix,eSet,character,missing-method Man page
genotypeMatrix,eSet,numeric,character-method Man page
[,GenotypeMatrix,index,index,missing-method Man page
[,GenotypeMatrix,index,missing,missing-method Man page
genotypeMatrix-methods Man page
[,GenotypeMatrix,missing,index,missing-method Man page
hg18Unmasked Man page
hg19Unmasked Man page
hg38Unmasked Man page
hgA Man page
invSdWeights Man page
length,NullModel-method Man page
logisticWeights Man page
MAF Man page
MAF,GenotypeMatrix-method Man page
MAF,VariantInfo-method Man page
method:genotypeMatrix Man page
method:readGenotypeMatrix Man page
method:readVariantInfo Man page
names,NullModel-method Man page
nullModel Man page
NullModel Man page
NullModel-class Man page
nullModel,formula,data.frame-method Man page
nullModel,formula,missing-method Man page
[,NullModel,index,missing,missing-method Man page
nullModel,matrix,factor-method Man page
nullModel,matrix,numeric-method Man page
nullModel-methods Man page
nullModel,missing,factor-method Man page
nullModel,missing,numeric-method Man page
p.adjust Man page
p.adjust,AssocTestResultRanges-method Man page
p.adjust-methods Man page
partitionRegions Man page
partitionRegions,GRangesList-method Man page
partitionRegions,GRanges-method Man page
partitionRegions,MaskedBSgenome-method Man page
partitionRegions-methods Man page
plot Man page
plot,AssocTestResultRanges,character-method Man page
plot,AssocTestResultRanges,GRanges-method Man page
plot,AssocTestResultRanges,missing-method Man page
plot,GenotypeMatrix,factor-method Man page
plot,GenotypeMatrix,missing-method Man page
plot,GenotypeMatrix,numeric-method Man page
plot,GRanges,character-method Man page
plot-methods Man page
podkat Man page
podkat-package Man page
print Man page
print,AssocTestResultRanges-method Man page
print-methods Man page
qqplot Man page
qqplot,AssocTestResultRanges,AssocTestResultRanges-method Man page
qqplot,AssocTestResultRanges,missing-method Man page
qqplot-methods Man page
readGenotypeMatrix Man page
readGenotypeMatrix,character,GRanges-method Man page
readGenotypeMatrix,character,missing-method Man page
readGenotypeMatrix-methods Man page
readGenotypeMatrix,TabixFile,GRanges-method Man page
readGenotypeMatrix,TabixFile,missing-method Man page
readRegionsFromBedFile Man page
readSampleNamesFromVcfHeader Man page
readVariantInfo Man page
readVariantInfo,character,GRanges-method Man page
readVariantInfo,character,missing-method Man page
readVariantInfo-methods Man page
readVariantInfo,TabixFile,GRanges-method Man page
readVariantInfo,TabixFile,missing-method Man page
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
unmasked-datasets Man page
unmaskedRegions Man page
variantInfo Man page
VariantInfo Man page
VariantInfo-class Man page
variantInfo,GenotypeMatrix-method Man page
variantInfo,GRanges-method Man page
variantInfo,missing-method Man page
weightFuncs Man page
weights Man page
weights,AssocTestResult-method Man page
weights,AssocTestResultRanges-method Man page
weights-methods Man page

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

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