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 1.10.0 (released on October 31, 2017, as part of Bioconductor 3.6). 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 3.6 requires R version 3.4.2.The current development version of the package is 1.11.0.
Documentation
Getting started
- To load the package, enter "library(podkat)" in your R session.
- To view the user manual, enter "vignette("podkat")".
- To do a first example, enter "example(podkat)".
User support
If you encounter any issues or if you have any question that might be of interest also for other users, before writing a private message to the package developers/maintainers, please consider posting on Bioconductor Support or StackOverflow. For all other matters regarding the package, please contact [email protected].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 (2017). PODKAT: An R Package for Association Testing Involving Rare and Private Variants. R package version 1.8.0.
Change log
- Version 1.10.0:
- release as part of Bioconductor 3.6
- Version 1.9.0:
- devel branch created from version 1.8.0
- Version 1.8.0:
- release as part of Bioconductor 3.5
- Version 1.7.0:
- new branch for Bioconductor 3.5 devel
- Version 1.6.0:
- release as part of Bioconductor 3.4
- Version 1.5.4:
- fix in vignette code that became necessary because of a change in the hg38 transcript annotation
- Version 1.5.3:
- readRegionsFromBedFile() now allows for including metadata columns
- corresponding changes in documentation
- fix of call to method rowRanges() into suggested package
- fix of citation info file
- fix of inst/NEWS
- Version 1.5.1 / 1.5.2:
- version number bumps for technical reasons related to Bioconductor build servers
- Version 1.5.0:
- new branch for Bioconductor 3.4 devel
- 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