semisup

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see semisup.

Detecting SNPs with interactive effects on a quantitative trait


Bioconductor version: 3.7

This R packages moves away from testing interaction terms, and move 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>

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

Installation

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


if (!require("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")
pkgdown HTML
pkgdown HTML
semisup PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, DNASeq, Genetics, GenomicVariation, Microarray, MultipleComparison, SNP, Software, SomaticMutation
Version 1.4.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.0.0)
Imports SummarizedExperiment, VGAM
System Requirements
URL https://github.com/rauschenberger/semisup
Bug Reports https://github.com/rauschenberger/semisup/issues
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Suggests knitr, testthat
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Package Archives

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

Source Package semisup_1.4.0.tar.gz
Windows Binary semisup_1.4.0.zip
Mac OS X 10.11 (El Capitan) semisup_1.4.0.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 https://bioconductor.org/packages/semisup/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive