martini
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see martini.
GWAS Incorporating Networks
Bioconductor version: 3.8
martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.
Author: Hector Climente-Gonzalez [aut, cre], Chloe-Agathe Azencott [aut]
Maintainer: Hector Climente-Gonzalez <hector.climente at curie.fr>
citation("martini")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("martini")
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("martini")| Running SConES | HTML | R Script |
| Simulating SConES-based phenotypes | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | FeatureExtraction, GeneticVariability, Genetics, GenomeWideAssociation, GraphAndNetwork, Network, SNP, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5) |
| Imports | igraph (>= 1.0.1), Matrix, methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats(>= 1.20.0), S4Vectors(>= 0.12.2), stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | biomaRt(>= 2.34.1), httr (>= 1.2.1), IRanges(>= 2.8.2), knitr, testthat, tidyverse, rmarkdown |
| Linking To | Rgin, Rcpp, RcppEigen (>= 0.3.3.3.0) |
| 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 | martini_1.2.0.tar.gz |
| Windows Binary | martini_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | martini_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/martini |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/martini |
| Bioc Package Browser | https://code.bioconductor.org/browse/martini/ |
| Package Short Url | https://bioconductor.org/packages/martini/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |