Position-Dependent Kernel Association Test

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Documentation for package ‘podkat’ version 1.32.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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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'