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' |