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podkat (version 1.4.2)

Position-Dependent Kernel Association Test

Description

This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

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Version

Version

1.4.2

License

GPL (>= 2)

Maintainer

Ulrich Bodenhofer

Last Published

February 15th, 2017

Functions in podkat (1.4.2)

filterResult-methods

Filter Association Test Results According to p-Values or Variants' Contributions
AssocTestResult-class

Class AssocTestResult
GenotypeMatrix-class

Class GenotypeMatrix
partitionRegions-methods

Partition Genomic Regions
VariantInfo-class

Class VariantInfo
readRegionsFromBedFile

Read Genomic Regions from BED File
AssocTestResultRanges-class

Class AssocTestResultRanges
NullModel-class

Class NullModel
p.adjust-methods

Adjust p-Value for Multiple Tests
print-methods

Print Association Test Results
weights

Extract Contribution Weights of Variants
readSampleNamesFromVcfHeader

Read Sample Names from VCF File Header
assocTest

Perform Association Test
podkat-package

PODKAT Package
readVariantInfo-methods

Read information about variants from VCF file
readGenotypeMatrix-methods

Read from VCF File
genotypeMatrix-methods

Constructors for Creating GenotypeMatrix Objects
sort-methods

Sort Association Test Results
computeKernel

Compute Kernel Matrix
plot

Plotting functions
hgA

Artificial Human Chromosome for Testing Purposes
weightFuncs

Weighting Functions
unmasked-datasets

Unmasked Regions of Human Genomes
split-methods

Split GRanges Object
qqplot

Quantile-Quantile Plots
unmaskedRegions

Extract Unmasked Regions from MaskedBSgenome Object
nullModel

Create Null Model for Association Test