genphen

DOI: 10.18129/B9.bioc.genphen    

A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models

Bioconductor version: Release (3.6)

Genetic association studies have become an essential tool for studying the relationship between genotypes and phenotypes. They are necessary for the discovery of disease-causing genetic variants. Here we provide a tool for conducting genetic association studies, which uses statistical learning techniques such as random forests and support vector machines, as well as using Bayesian inference with Bayesian hierarchical models. These techniques are superior to the commonly used (frequentist) statistical approaches, alleviating the multiple hypothesis problems and the need for P value corrections, which often lead to massive numbers of false negatives. Thus, with genphen we provide a framework to compare the results obtained using frequentist methods with those obtained using the more sophisticated methods provided by this tool. The tool also provides a few visualization functions which enable the user to inspect the results of such genetic association study and conveniently select the genotypes which have the highest strength of association with the phenotype.

Author: Simo Kitanovski

Maintainer: Simo Kitanovski <simo.kitanovski at uni-due.de>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("genphen")

 

PDF	R Script	genphen overview
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Classification, FeatureExtraction, Genetics, GenomeWideAssociation, Regression, SequenceMatching, Sequencing, Software, SupportVectorMachine
Version	1.6.0
In Bioconductor since	BioC 3.3 (R-3.3) (2 years)
License	GPL (>= 2)
Depends	R (>= 3.3), randomForest, e1071, ggplot2, effsize, Biostrings, rjags
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	genphen_1.6.0.tar.gz
Windows Binary	genphen_1.6.0.zip
Mac OS X 10.11 (El Capitan)	genphen_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genphen
Package Short Url	http://bioconductor.org/packages/genphen/
Package Downloads Report	Download Stats