| podkat-package | PODKAT Package |
| assocTest | Perform Association Test |
| assocTest-method | Perform Association Test |
| assocTest-methods | Perform Association Test |
| AssocTestResult | Class 'AssocTestResult' |
| AssocTestResult-class | Class 'AssocTestResult' |
| AssocTestResultRanges | Class 'AssocTestResultRanges' |
| AssocTestResultRanges-class | Class 'AssocTestResultRanges' |
| b36Unmasked | Unmasked Regions of Human Genomes |
| b37Unmasked | Unmasked Regions of Human Genomes |
| betaWeights | Weighting Functions |
| c-method | Class 'AssocTestResultRanges' |
| class:AssocTestResult | Class 'AssocTestResult' |
| class:AssocTestResultRanges | Class 'AssocTestResultRanges' |
| class:GenotypeMatrix | Class 'GenotypeMatrix' |
| class:NullModel | Class 'NullModel' |
| class:VariantInfo | Class 'VariantInfo' |
| coefficients-method | Class 'NullModel' |
| computeKernel | Compute Kernel Matrix |
| filterResult | Filter Association Test Results According to p-Values or Variants' Contributions |
| filterResult-method | Filter Association Test Results According to p-Values or Variants' Contributions |
| filterResult-methods | Filter Association Test Results According to p-Values or Variants' Contributions |
| GenotypeMatrix | Class 'GenotypeMatrix' |
| genotypeMatrix | Constructors for Creating 'GenotypeMatrix' Objects |
| GenotypeMatrix-class | Class 'GenotypeMatrix' |
| genotypeMatrix-method | Constructors for Creating 'GenotypeMatrix' Objects |
| genotypeMatrix-methods | Constructors for Creating 'GenotypeMatrix' Objects |
| 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 |
| invSdWeights | Weighting Functions |
| length-method | Class 'NullModel' |
| logisticWeights | Weighting Functions |
| MAF | Class 'VariantInfo' |
| MAF-method | Class 'GenotypeMatrix' |
| MAF-method | Class 'VariantInfo' |
| method:genotypeMatrix | Constructors for Creating 'GenotypeMatrix' Objects |
| method:readGenotypeMatrix | Read from VCF File |
| method:readVariantInfo | Read information about variants from VCF file |
| names-method | Class 'NullModel' |
| NullModel | Class 'NullModel' |
| nullModel | Create Null Model for Association Test |
| NullModel-class | Class 'NullModel' |
| nullModel-method | Create Null Model for Association Test |
| nullModel-methods | Create Null Model for Association Test |
| p.adjust | Adjust p-Value for Multiple Tests |
| p.adjust-method | Adjust p-Value for Multiple Tests |
| p.adjust-methods | Adjust p-Value for Multiple Tests |
| partitionRegions | Partition Genomic Regions |
| partitionRegions-method | Partition Genomic Regions |
| partitionRegions-methods | Partition Genomic Regions |
| plot | Plotting functions |
| plot-method | Plotting functions |
| plot-methods | Plotting functions |
| podkat | PODKAT Package |
| Print Association Test Results | |
| print-method | Print Association Test Results |
| print-methods | Print Association Test Results |
| qqplot | Quantile-Quantile Plots |
| qqplot-method | Quantile-Quantile Plots |
| qqplot-methods | Quantile-Quantile Plots |
| readGenotypeMatrix | Read from VCF File |
| readGenotypeMatrix-method | Read from VCF File |
| readGenotypeMatrix-methods | Read from VCF File |
| readRegionsFromBedFile | Read Genomic Regions from BED File |
| readSampleNamesFromVcfHeader | Read Sample Names from VCF File Header |
| readVariantInfo | Read information about variants from VCF file |
| readVariantInfo-method | Read information about variants from VCF file |
| readVariantInfo-methods | Read information about variants from VCF file |
| residuals-method | Class 'NullModel' |
| show-method | Class 'AssocTestResult' |
| show-method | Class 'AssocTestResultRanges' |
| show-method | Class 'GenotypeMatrix' |
| show-method | Class 'NullModel' |
| show-method | Class 'VariantInfo' |
| sort | Sort Association Test Results |
| sort-method | Sort Association Test Results |
| sort-methods | Sort Association Test Results |
| split | Split 'GRanges' Object |
| split-method | Split 'GRanges' Object |
| split-methods | Split 'GRanges' Object |
| summary-method | Class 'VariantInfo' |
| unmasked-datasets | Unmasked Regions of Human Genomes |
| unmaskedRegions | Extract Unmasked Regions from 'MaskedBSgenome' Object |
| VariantInfo | Class 'VariantInfo' |
| variantInfo | Class 'VariantInfo' |
| VariantInfo-class | Class 'VariantInfo' |
| variantInfo-method | Class 'GenotypeMatrix' |
| variantInfo-method | Class 'VariantInfo' |
| weightFuncs | Weighting Functions |
| weights | Extract Contribution Weights of Variants |
| weights-method | Extract Contribution Weights of Variants |
| weights-methods | Extract Contribution Weights of Variants |
| [-method | Class 'GenotypeMatrix' |
| [-method | Class 'NullModel' |