podkat

This is the development version of podkat; for the stable release version, see podkat.

Position-Dependent Kernel Association Test

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DOI: 10.18129/B9.bioc.podkat

Bioconductor version: Development (3.23)

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.

Author: Ulrich Bodenhofer [aut, cre]

Maintainer: Ulrich Bodenhofer <ulrich at bodenhofer.com>

Citation (from within R, enter citation("podkat")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("podkat")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("podkat")

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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome

Version 1.43.0

In Bioconductor since BioC 3.1 (R-3.2) (10.5 years)

License GPL (>= 2)

Depends R (>= 3.5.0), methods, Rsamtools(>= 1.99.1), GenomicRanges

Imports Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, Seqinfo, IRanges, Biostrings, BSgenome(>= 1.32.0)

System Requirements GNU make

URL https://github.com/UBod/podkat

Suggests BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools(>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr

Linking To Rcpp, Rhtslib(>= 1.15.3)

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