Package: podkat 1.45.0

Ulrich Bodenhofer

podkat: Position-Dependent Kernel Association Test

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.

Authors:Ulrich Bodenhofer [aut, cre]

podkat_1.45.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
podkat/json (API)

# Install 'podkat' in R:

install.packages('podkat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ubod/podkat/issues

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library
c++– GNU Standard C++ Library v3

Datasets:

b36Unmasked - Unmasked Regions of Human Genomes
b37Unmasked - Unmasked Regions of Human Genomes
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

On BioConductor:podkat-1.45.0(bioc 3.24)podkat-1.44.0(bioc 3.23)

genetics wholegenome annotation variantannotation sequencing dataimport curl bzip2 xz-utils zlib cpp

5.24 score 6 scripts 442 downloads 1 mentions 25 exports 51 dependencies

Last updated from:a5ee2c4653. Checks:1 WARNING, 11 NOTE, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	398
linux-devel-arm64	NOTE	492
linux-devel-x86_64	NOTE	582
source / vignettes	OK	620
linux-release-arm64	NOTE	498
linux-release-x86_64	NOTE	640
macos-release-arm64	NOTE	425
macos-release-x86_64	NOTE	1078
macos-oldrel-arm64	NOTE	504
macos-oldrel-x86_64	NOTE	619
windows-devel	NOTE	645
windows-release	NOTE	617
windows-oldrel	NOTE	622
wasm-release	FAIL	348

Exports:assocTest betaWeights coefficients computeKernel filterResult genotypeMatrix invSdWeights logisticWeights MAF nullModel p.adjust partitionRegions print qqplot readGenotypeMatrix readRegionsFromBedFile readSampleNamesFromVcfHeader readVariantInfo show sort split summary unmaskedRegions variantInfo weights

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cigarillo codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys XML XVector yaml

PODKAT - An R Package for Association Testing Involving Rare and Private Variants

Rendered frompodkat.Rnwusingknitr::knitr

Last update: 2024-04-23
Started: 2015-03-31

Help page	Topics
PODKAT Package	podkat-package podkat
Perform Association Test	assocTest assocTest,character,NullModel-method assocTest,GenotypeMatrix,NullModel-method assocTest,matrix,NullModel-method assocTest,TabixFile,NullModel-method assocTest-methods
Class 'AssocTestResult'	AssocTestResult AssocTestResult-class class:AssocTestResult show,AssocTestResult-method
Class 'AssocTestResultRanges'	AssocTestResultRanges AssocTestResultRanges-class c,AssocTestResultRanges-method class:AssocTestResultRanges show,AssocTestResultRanges-method
Compute Kernel Matrix	computeKernel
Filter Association Test Results According to p-Values or Variants' Contributions	filterResult filterResult,AssocTestResultRanges-method filterResult,GRanges-method filterResult,GRangesList-method filterResult-methods
Class 'GenotypeMatrix'	class:GenotypeMatrix GenotypeMatrix GenotypeMatrix-class MAF,GenotypeMatrix-method show,GenotypeMatrix-method variantInfo,GenotypeMatrix-method [,GenotypeMatrix,index,index,missing-method [,GenotypeMatrix,index,missing,missing-method [,GenotypeMatrix,missing,index,missing-method
Constructors for Creating 'GenotypeMatrix' Objects	genotypeMatrix genotypeMatrix,ANY,character,missing-method genotypeMatrix,ANY,GRanges,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
Artificial Human Chromosome for Testing Purposes	hgA
Create Null Model for Association Test	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
Class 'NullModel'	class:NullModel coefficients,NullModel-method length,NullModel-method names,NullModel-method NullModel NullModel-class residuals,NullModel-method show,NullModel-method [,NullModel,index,missing,missing-method
Adjust p-Value for Multiple Tests	p.adjust p.adjust,AssocTestResultRanges-method p.adjust-methods
Partition Genomic Regions	partitionRegions partitionRegions,GRanges-method partitionRegions,GRangesList-method partitionRegions,MaskedBSgenome-method partitionRegions-methods
Plotting functions	plot plot,AssocTestResultRanges,character-method plot,AssocTestResultRanges,GRanges-method plot,AssocTestResultRanges,missing-method plot,GenotypeMatrix,factor-method plot,GenotypeMatrix,missing-method plot,GenotypeMatrix,numeric-method plot,GRanges,character-method plot-methods
Print Association Test Results	print print,AssocTestResultRanges-method print-methods
Quantile-Quantile Plots	qqplot qqplot,AssocTestResultRanges,AssocTestResultRanges-method qqplot,AssocTestResultRanges,missing-method qqplot-methods
Read from VCF File	method:readGenotypeMatrix readGenotypeMatrix readGenotypeMatrix,character,GRanges-method readGenotypeMatrix,character,missing-method readGenotypeMatrix,TabixFile,GRanges-method readGenotypeMatrix,TabixFile,missing-method readGenotypeMatrix-methods
Read Genomic Regions from BED File	readRegionsFromBedFile
Read Sample Names from VCF File Header	readSampleNamesFromVcfHeader
Read information about variants from VCF file	method:readVariantInfo readVariantInfo readVariantInfo,character,GRanges-method readVariantInfo,character,missing-method readVariantInfo,TabixFile,GRanges-method readVariantInfo,TabixFile,missing-method readVariantInfo-methods
Sort Association Test Results	sort sort,AssocTestResultRanges-method sort-methods
Split 'GRanges' Object	split split,GRanges,GRangesList-method split-methods
Unmasked Regions of Human Genomes	b36Unmasked b37Unmasked hg18Unmasked hg19Unmasked hg38Unmasked unmasked-datasets
Extract Unmasked Regions from 'MaskedBSgenome' Object	unmaskedRegions
Class 'VariantInfo'	class:VariantInfo MAF MAF,VariantInfo-method show,VariantInfo-method summary,VariantInfo-method VariantInfo variantInfo variantInfo,GRanges-method variantInfo,missing-method VariantInfo-class
Weighting Functions	betaWeights invSdWeights logisticWeights weightFuncs
Extract Contribution Weights of Variants	weights weights,AssocTestResult-method weights,AssocTestResultRanges-method weights-methods

Package: podkat 1.45.0

podkat: Position-Dependent Kernel Association Test

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