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("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 | R Script | |
| Reference Manual | ||
| 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 |
See More
| Suggests | knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |