semisup

DOI: 10.18129/B9.bioc.semisup    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see semisup.

Semi-Supervised Mixture Model

Bioconductor version: 3.8

Useful for detecting SNPs with interactive effects on a quantitative trait. This R packages moves away from testing interaction terms, and moves towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in distribution between some individuals in one group and all other individuals, it possibly has an interactive effect. Implicitly, the membership probabilities may suggest potential interacting variables.

Author: Armin Rauschenberger [aut, cre]

Maintainer: Armin Rauschenberger <a.rauschenberger at vumc.nl>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("semisup")

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("semisup")

 

HTML		pkgdown
HTML		pkgdown
PDF	R Script	semisup
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, DNASeq, Genetics, GenomicVariation, Microarray, MultipleComparison, SNP, Software, SomaticMutation
Version	1.6.0
In Bioconductor since	BioC 3.5 (R-3.4) (2 years)
License	GPL-3
Depends	R (>= 3.0.0)
Imports	SummarizedExperiment, VGAM
LinkingTo
Suggests	knitr, testthat
SystemRequirements
Enhances
URL	https://github.com/rauschenberger/semisup
BugReports	https://github.com/rauschenberger/semisup/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	semisup_1.6.0.tar.gz
Windows Binary	semisup_1.6.0.zip
Mac OS X 10.11 (El Capitan)	semisup_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/semisup
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/semisup
Package Short Url	http://bioconductor.org/packages/semisup/
Package Downloads Report	Download Stats