Position-Dependent Kernel Association Test

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Documentation for package ‘podkat’ version 1.22.0

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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'