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

The podkat 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.

Installation

The R package podkat is available from Bioconductor. The first version of the package has been released as part of Bioconductor 3.1 on April 17, 2015. The current version of the package is 1.4.0 (released on May 4, 2016, as part of Bioconductor 3.3). To install podkat, follow the simple standard procedure for installing Bioconductor packages i.e. enter the following into your R session:
source("http://www.bioconductor.org/biocLite.R")
biocLite("podkat")
Please note that Bioconductor 3.3 requires R version 3.3.0.

The current development version of the package is 1.5.0.

Documentation

  1. User Manual: PDF
  2. Reference Manual: PDF

Getting started

  1. To load the package, enter "library(podkat)" in your R session.
  2. To view the user manual, enter "vignette("podkat")".
  3. To do a first example, enter "example(podkat)".

Citing this package

If you use this package for research that is published later, you are kindly asked to cite it as follows:

U. Bodenhofer (2016). PODKAT: An R Package for Association Testing Involving Rare and Private Variants. R package version 1.4.0.

Change log

Version 1.4.0:
release as part of Bioconductor 3.3
Version 1.3.1:
  • added missing method readVariantInfo() for signature "character", "cGRanges"
  • minor streamlining of source code of readGenotypeMatrix()
  • corrections of namespace imports
Version 1.3.0:
new branch for Bioconductor 3.3 devel
Version 1.2.0:
release as part of Bioconductor 3.2
Version 1.1.3:
  • further fix of weights() method for signature 'AssocTestResultRanges'
Version 1.1.2:
  • fix of weights() method for signature 'AssocTestResultRanges'
Version 1.1.1:
  • fix of filterResults() method for signature 'GRanges'
Version 1.1.0:
new branch for Bioconductor 3.2 devel
Version 1.0.0:
first official release as part of Bioconductor 3.1

Contact

For suggestions, bug reports, and other matters regarding the package, please contact podkat@bioinf.jku.at.