# Position-Dependent Kernel Association Test

## Documentation for package ‘podkat’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 | 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'