Package: podkat 1.39.0
Ulrich Bodenhofer
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.
Authors:
podkat_1.39.0.tar.gz
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podkat.pdf |podkat.html✨
podkat/json (API)
NEWS
| # Install 'podkat' in R: |
| install.packages('podkat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ubod/podkat/issues
- b36Unmasked - Unmasked Regions of Human Genomes
- b37Unmasked - Unmasked Regions of Human Genomes
- hg18Unmasked - Unmasked Regions of Human Genomes
- hg19Unmasked - Unmasked Regions of Human Genomes
- hg38Unmasked - Unmasked Regions of Human Genomes
- hgA - Artificial Human Chromosome for Testing Purposes
On BioConductor:podkat-1.39.0(bioc 3.21)podkat-1.38.0(bioc 3.20)
geneticswholegenomeannotationvariantannotationsequencingdataimportcurlbzip2xz-utilszlibcpp
Last updated 2 months agofrom:ff139de798. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 30 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 30 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 30 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 30 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 30 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 30 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 30 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 30 2024 |
Exports:assocTestbetaWeightscoefficientscomputeKernelfilterResultgenotypeMatrixinvSdWeightslogisticWeightsMAFnullModelp.adjustpartitionRegionsprintqqplotreadGenotypeMatrixreadRegionsFromBedFilereadSampleNamesFromVcfHeaderreadVariantInfoshowsortsplitsummaryunmaskedRegionsvariantInfoweights
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppRCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| PODKAT Package | podkat-package podkat |
| Perform Association Test | assocTest assocTest,character,NullModel-method assocTest,GenotypeMatrix,NullModel-method assocTest,matrix,NullModel-method assocTest,TabixFile,NullModel-method assocTest-methods |
| Class 'AssocTestResult' | AssocTestResult AssocTestResult-class class:AssocTestResult show,AssocTestResult-method |
| Class 'AssocTestResultRanges' | AssocTestResultRanges AssocTestResultRanges-class c,AssocTestResultRanges-method class:AssocTestResultRanges show,AssocTestResultRanges-method |
| Compute Kernel Matrix | computeKernel |
| Filter Association Test Results According to p-Values or Variants' Contributions | filterResult filterResult,AssocTestResultRanges-method filterResult,GRanges-method filterResult,GRangesList-method filterResult-methods |
| Class 'GenotypeMatrix' | class:GenotypeMatrix GenotypeMatrix GenotypeMatrix-class MAF,GenotypeMatrix-method show,GenotypeMatrix-method variantInfo,GenotypeMatrix-method [,GenotypeMatrix,index,index,missing-method [,GenotypeMatrix,index,missing,missing-method [,GenotypeMatrix,missing,index,missing-method |
| Constructors for Creating 'GenotypeMatrix' Objects | genotypeMatrix genotypeMatrix,ANY,character,missing-method genotypeMatrix,ANY,GRanges,missing-method genotypeMatrix,ANY,missing,missing-method genotypeMatrix,ANY,numeric,character-method genotypeMatrix,eSet,character,character-method genotypeMatrix,eSet,character,missing-method genotypeMatrix,eSet,numeric,character-method genotypeMatrix-methods method:genotypeMatrix |
| Artificial Human Chromosome for Testing Purposes | hgA |
| Create Null Model for Association Test | nullModel nullModel,formula,data.frame-method nullModel,formula,missing-method nullModel,matrix,factor-method nullModel,matrix,numeric-method nullModel,missing,factor-method nullModel,missing,numeric-method nullModel-methods |
| Class 'NullModel' | class:NullModel coefficients,NullModel-method length,NullModel-method names,NullModel-method NullModel NullModel-class residuals,NullModel-method show,NullModel-method [,NullModel,index,missing,missing-method |
| Adjust p-Value for Multiple Tests | p.adjust p.adjust,AssocTestResultRanges-method p.adjust-methods |
| Partition Genomic Regions | partitionRegions partitionRegions,GRanges-method partitionRegions,GRangesList-method partitionRegions,MaskedBSgenome-method partitionRegions-methods |
| Plotting functions | plot plot,AssocTestResultRanges,character-method plot,AssocTestResultRanges,GRanges-method plot,AssocTestResultRanges,missing-method plot,GenotypeMatrix,factor-method plot,GenotypeMatrix,missing-method plot,GenotypeMatrix,numeric-method plot,GRanges,character-method plot-methods |
| Print Association Test Results | print print,AssocTestResultRanges-method print-methods |
| Quantile-Quantile Plots | qqplot qqplot,AssocTestResultRanges,AssocTestResultRanges-method qqplot,AssocTestResultRanges,missing-method qqplot-methods |
| Read from VCF File | method:readGenotypeMatrix readGenotypeMatrix readGenotypeMatrix,character,GRanges-method readGenotypeMatrix,character,missing-method readGenotypeMatrix,TabixFile,GRanges-method readGenotypeMatrix,TabixFile,missing-method readGenotypeMatrix-methods |
| Read Genomic Regions from BED File | readRegionsFromBedFile |
| Read Sample Names from VCF File Header | readSampleNamesFromVcfHeader |
| Read information about variants from VCF file | method:readVariantInfo readVariantInfo readVariantInfo,character,GRanges-method readVariantInfo,character,missing-method readVariantInfo,TabixFile,GRanges-method readVariantInfo,TabixFile,missing-method readVariantInfo-methods |
| Sort Association Test Results | sort sort,AssocTestResultRanges-method sort-methods |
| Split 'GRanges' Object | split split,GRanges,GRangesList-method split-methods |
| Unmasked Regions of Human Genomes | b36Unmasked b37Unmasked hg18Unmasked hg19Unmasked hg38Unmasked unmasked-datasets |
| Extract Unmasked Regions from 'MaskedBSgenome' Object | unmaskedRegions |
| Class 'VariantInfo' | class:VariantInfo MAF MAF,VariantInfo-method show,VariantInfo-method summary,VariantInfo-method VariantInfo variantInfo variantInfo,GRanges-method variantInfo,missing-method VariantInfo-class |
| Weighting Functions | betaWeights invSdWeights logisticWeights weightFuncs |
| Extract Contribution Weights of Variants | weights weights,AssocTestResult-method weights,AssocTestResultRanges-method weights-methods |
