To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("podkat")

In most cases, you don't need to download the package archive at all.

podkat

DOI: 10.18129/B9.bioc.podkat    

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

Position-Dependent Kernel Association Test

Bioconductor version: Development (3.7)

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

Maintainer: Ulrich Bodenhofer <bodenhofer at bioinf.jku.at>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("podkat")

Documentation

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

browseVignettes("podkat")

 

PDF R Script PODKAT - An R Package for Association Testing Involving Rare and Private Variants
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation, WholeGenome
Version 1.11.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License GPL (>= 2)
Depends R (>= 3.2.0), methods, Rsamtools, GenomicRanges
Imports Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome(>= 1.32.0)
LinkingTo Rcpp, Rsamtools
Suggests BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools(>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr
SystemRequirements
Enhances
URL http://www.bioinf.jku.at/software/podkat/
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package podkat_1.11.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) podkat_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/podkat
Package Short Url http://bioconductor.org/packages/podkat/
Package Downloads Report Download Stats

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