{
  "_id": "6a1938c2acfb0bcc41dd36fd",
  "Package": "podkat",
  "Type": "Package",
  "Title": "Position-Dependent Kernel Association Test",
  "Version": "1.44.0",
  "Date": "2025-09-19",
  "Authors@R": "c(person(given = \"Ulrich\",\nfamily = \"Bodenhofer\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ulrich@bodenhofer.com\"))",
  "Maintainer": "Ulrich Bodenhofer <ulrich@bodenhofer.com>",
  "Description": "This package provides an association test that is capable\nof dealing with very rare and even private variants. This is\naccomplished by a kernel-based approach that takes the\npositions of the variants into account. The test can be used\nfor pre-processed matrix data, but also directly for variant\ndata stored in VCF files. Association testing can be performed\nwhole-genome, whole-exome, or restricted to pre-defined regions\nof interest. The test is complemented by tools for analyzing\nand visualizing the results.",
  "URL": "https://github.com/UBod/podkat",
  "License": "GPL (>= 2)",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "Collate": "AllGenerics.R AllClasses.R inputChecks.R sort-methods.R\nshow-methods.R print-methods.R summary-methods.R\np.adjust-methods.R c-methods.R access-methods.R\ncoerce-methods.R resampling.R unmaskedRegions.R\npartitionRegions-methods.R genotypeMatrix-methods.R\ncomputeKernel.R computePvalues.R readGenotypeMatrix-methods.R\nreadVariantInfo-methods.R readSampleNamesFromVcfHeader.R\nreadRegionsFromBedFile.R weightFuncs.R assocTest-methods.R\nnullModel-methods.R qqplot-methods.R plot-methods.R\nfilterResult-methods.R split-methods.R computeWeights.R\nweights-methods.R",
  "biocViews": "Genetics, WholeGenome, Annotation, VariantAnnotation,\nSequencing, DataImport",
  "NeedsCompilation": "yes",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:56 UTC",
  "RemoteUrl": "https://github.com/bioc/podkat",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "2d5305c72893524a9c21501895a49da3bffd8b18",
  "Packaged": {
    "Date": "2026-05-29 06:12:48 UTC",
    "User": "root"
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  "Author": "Ulrich Bodenhofer [aut, cre]",
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  "_created": "2026-05-29T06:12:48.000Z",
  "_published": "2026-05-29T06:57:06.032Z",
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    "description": "Professor for Artificial Intelligence at University of Applied Sciences Upper Austria / Chief Artificial Intelligence Officer at QUOMATIC.AI",
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    "MAF",
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    "readRegionsFromBedFile",
    "readSampleNamesFromVcfHeader",
    "readVariantInfo",
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    "sort",
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    "unmaskedRegions",
    "variantInfo",
    "weights"
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  "_datasets": [
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      "title": "Unmasked Regions of Human Genomes",
      "object": "b36Unmasked",
      "file": "b36Unmasked.RData",
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      "title": "Unmasked Regions of Human Genomes",
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      "title": "Unmasked Regions of Human Genomes",
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      "title": "Artificial Human Chromosome for Testing Purposes",
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      "table": false,
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      "page": "podkat-package",
      "title": "PODKAT Package",
      "topics": [
        "podkat-package",
        "podkat"
      ]
    },
    {
      "page": "assocTest-methods",
      "title": "Perform Association Test",
      "topics": [
        "assocTest",
        "assocTest,character,NullModel-method",
        "assocTest,GenotypeMatrix,NullModel-method",
        "assocTest,matrix,NullModel-method",
        "assocTest,TabixFile,NullModel-method",
        "assocTest-methods"
      ]
    },
    {
      "page": "AssocTestResult-class",
      "title": "Class 'AssocTestResult'",
      "topics": [
        "AssocTestResult",
        "AssocTestResult-class",
        "class:AssocTestResult",
        "show,AssocTestResult-method"
      ]
    },
    {
      "page": "AssocTestResultRanges-class",
      "title": "Class 'AssocTestResultRanges'",
      "topics": [
        "AssocTestResultRanges",
        "AssocTestResultRanges-class",
        "c,AssocTestResultRanges-method",
        "class:AssocTestResultRanges",
        "show,AssocTestResultRanges-method"
      ]
    },
    {
      "page": "computeKernel",
      "title": "Compute Kernel Matrix",
      "topics": [
        "computeKernel"
      ]
    },
    {
      "page": "filterResult-methods",
      "title": "Filter Association Test Results According to p-Values or Variants' Contributions",
      "topics": [
        "filterResult",
        "filterResult,AssocTestResultRanges-method",
        "filterResult,GRanges-method",
        "filterResult,GRangesList-method",
        "filterResult-methods"
      ]
    },
    {
      "page": "GenotypeMatrix-class",
      "title": "Class 'GenotypeMatrix'",
      "topics": [
        "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"
      ]
    },
    {
      "page": "genotypeMatrix-methods",
      "title": "Constructors for Creating 'GenotypeMatrix' Objects",
      "topics": [
        "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"
      ]
    },
    {
      "page": "hgA",
      "title": "Artificial Human Chromosome for Testing Purposes",
      "topics": [
        "hgA"
      ]
    },
    {
      "page": "nullModel-methods",
      "title": "Create Null Model for Association Test",
      "topics": [
        "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"
      ]
    },
    {
      "page": "NullModel-class",
      "title": "Class 'NullModel'",
      "topics": [
        "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"
      ]
    },
    {
      "page": "p.adjust-methods",
      "title": "Adjust p-Value for Multiple Tests",
      "topics": [
        "p.adjust",
        "p.adjust,AssocTestResultRanges-method",
        "p.adjust-methods"
      ]
    },
    {
      "page": "partitionRegions-methods",
      "title": "Partition Genomic Regions",
      "topics": [
        "partitionRegions",
        "partitionRegions,GRanges-method",
        "partitionRegions,GRangesList-method",
        "partitionRegions,MaskedBSgenome-method",
        "partitionRegions-methods"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Plotting functions",
      "topics": [
        "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"
      ]
    },
    {
      "page": "print-methods",
      "title": "Print Association Test Results",
      "topics": [
        "print",
        "print,AssocTestResultRanges-method",
        "print-methods"
      ]
    },
    {
      "page": "qqplot-methods",
      "title": "Quantile-Quantile Plots",
      "topics": [
        "qqplot",
        "qqplot,AssocTestResultRanges,AssocTestResultRanges-method",
        "qqplot,AssocTestResultRanges,missing-method",
        "qqplot-methods"
      ]
    },
    {
      "page": "readGenotypeMatrix-methods",
      "title": "Read from VCF File",
      "topics": [
        "method:readGenotypeMatrix",
        "readGenotypeMatrix",
        "readGenotypeMatrix,character,GRanges-method",
        "readGenotypeMatrix,character,missing-method",
        "readGenotypeMatrix,TabixFile,GRanges-method",
        "readGenotypeMatrix,TabixFile,missing-method",
        "readGenotypeMatrix-methods"
      ]
    },
    {
      "page": "readRegionsFromBedFile",
      "title": "Read Genomic Regions from BED File",
      "topics": [
        "readRegionsFromBedFile"
      ]
    },
    {
      "page": "readSampleNamesFromVcfHeader",
      "title": "Read Sample Names from VCF File Header",
      "topics": [
        "readSampleNamesFromVcfHeader"
      ]
    },
    {
      "page": "readVariantInfo-methods",
      "title": "Read information about variants from VCF file",
      "topics": [
        "method:readVariantInfo",
        "readVariantInfo",
        "readVariantInfo,character,GRanges-method",
        "readVariantInfo,character,missing-method",
        "readVariantInfo,TabixFile,GRanges-method",
        "readVariantInfo,TabixFile,missing-method",
        "readVariantInfo-methods"
      ]
    },
    {
      "page": "sort-methods",
      "title": "Sort Association Test Results",
      "topics": [
        "sort",
        "sort,AssocTestResultRanges-method",
        "sort-methods"
      ]
    },
    {
      "page": "split-methods",
      "title": "Split 'GRanges' Object",
      "topics": [
        "split",
        "split,GRanges,GRangesList-method",
        "split-methods"
      ]
    },
    {
      "page": "unmasked-datasets",
      "title": "Unmasked Regions of Human Genomes",
      "topics": [
        "b36Unmasked",
        "b37Unmasked",
        "hg18Unmasked",
        "hg19Unmasked",
        "hg38Unmasked",
        "unmasked-datasets"
      ]
    },
    {
      "page": "unmaskedRegions",
      "title": "Extract Unmasked Regions from 'MaskedBSgenome' Object",
      "topics": [
        "unmaskedRegions"
      ]
    },
    {
      "page": "VariantInfo-class",
      "title": "Class 'VariantInfo'",
      "topics": [
        "class:VariantInfo",
        "MAF",
        "MAF,VariantInfo-method",
        "show,VariantInfo-method",
        "summary,VariantInfo-method",
        "VariantInfo",
        "variantInfo",
        "variantInfo,GRanges-method",
        "variantInfo,missing-method",
        "VariantInfo-class"
      ]
    },
    {
      "page": "weightFuncs",
      "title": "Weighting Functions",
      "topics": [
        "betaWeights",
        "invSdWeights",
        "logisticWeights",
        "weightFuncs"
      ]
    },
    {
      "page": "weights-methods",
      "title": "Extract Contribution Weights of Variants",
      "topics": [
        "weights",
        "weights,AssocTestResult-method",
        "weights,AssocTestResultRanges-method",
        "weights-methods"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/podkat/raw/RELEASE_3_23/README.md",
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