Last data update: 2014.03.03
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CranContrib
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S4 class for storing the result of an association test for a single genomic region
● Data Source:
BioConductor
● Keywords: classes
● Alias: AssocTestResult, AssocTestResult-class, class:AssocTestResult, show,AssocTestResult-method
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S4 class for storing the result of an association test performed on multiple genomic regions
● Data Source:
BioConductor
● Keywords: classes
● Alias: AssocTestResultRanges, AssocTestResultRanges-class, c,AssocTestResultRanges-method, class:AssocTestResultRanges, show,AssocTestResultRanges-method
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1 images
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S4 class for storing genotypes efficiently as column-oriented sparse matrices along with variant info
● Data Source:
BioConductor
● Keywords: classes
● Alias: GenotypeMatrix, GenotypeMatrix-class, MAF,GenotypeMatrix-method, [,GenotypeMatrix,index,index,missing-method, [,GenotypeMatrix,index,missing,missing-method, [,GenotypeMatrix,missing,index,missing-method, class:GenotypeMatrix, show,GenotypeMatrix-method, variantInfo,GenotypeMatrix-method
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S4 class for storing null models for later usage with the assocTest method
● Data Source:
BioConductor
● Keywords: classes
● Alias: NullModel, NullModel-class, [,NullModel,index,missing,missing-method, class:NullModel, coefficients,NullModel-method, length,NullModel-method, names,NullModel-method, residuals,NullModel-method, show,NullModel-method
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S4 class for storing information about variants
● Data Source:
BioConductor
● Keywords: classes
● Alias: MAF, MAF,VariantInfo-method, VariantInfo, VariantInfo-class, class:VariantInfo, show,VariantInfo-method, summary,VariantInfo-method, variantInfo,GRanges-method, variantInfo,missing-method
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assocTest
(Package: podkat) :
Perform Association Test
Method for performing a kernel-based association test given a genotype, VCF file, or kernel matrix
● Data Source:
BioConductor
● Keywords: methods
● Alias: assocTest, assocTest,GenotypeMatrix,NullModel-method, assocTest,TabixFile,NullModel-method, assocTest,character,NullModel-method, assocTest,matrix,NullModel-method, assocTest-methods
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2 images
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Computes kernel matrix for a given genotype matrix
● Data Source:
BioConductor
● Keywords:
● Alias: computeKernel
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filterResult-methods
(Package: podkat) :
Filter Association Test Results According to p-Values or
Given an AssocTestResultRanges object, this method filters regions according to p-values or variants' contributions.
● Data Source:
BioConductor
● Keywords: methods
● Alias: filterResult, filterResult,AssocTestResultRanges-method, filterResult,GRanges-method, filterResult,GRangesList-method, filterResult-methods
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genotypeMatrix-methods
(Package: podkat) :
Constructors for Creating code{linkS4class{GenotypeMatrix
Create GenotypeMatrix object from (sparse) matrix object and positions of variants
● Data Source:
BioConductor
● Keywords: methods
● Alias: genotypeMatrix, genotypeMatrix,ANY,GRanges,missing-method, genotypeMatrix,ANY,character,missing-method, genotypeMatrix,ANY,missing,missing-method, genotypeMatrix,ANY,numeric,character-method, genotypeMatrix,eSet,character,character-method, genotypeMatrix,eSet,character,missing-method, genotypeMatrix,eSet,numeric,character-method, genotypeMatrix-methods, method:genotypeMatrix
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nullModel
(Package: podkat) :
Create Null Model for Association Test
Method for creating a null model that can be used for association testing using assocTest
● Data Source:
BioConductor
● Keywords: methods
● Alias: nullModel, nullModel,formula,data.frame-method, nullModel,formula,missing-method, nullModel,matrix,factor-method, nullModel,matrix,numeric-method, nullModel,missing,factor-method, nullModel,missing,numeric-method, nullModel-methods
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