podkat: Position-Dependent Kernel Association Test

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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.

Author
Ulrich Bodenhofer
Date of publication
None
Maintainer
Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
License
GPL (>= 2)
Version
1.6.0
URLs

View on Bioconductor

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

Files in this package

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