martini

DOI: 10.18129/B9.bioc.martini  

GWAS Incorporating Networks

Bioconductor version: Release (3.16)

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 riken.jp>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Running SConES
HTML	R Script	Simulating SConES-based phenotypes
PDF		Reference Manual

Details

biocViews	FeatureExtraction, GeneticVariability, Genetics, GenomeWideAssociation, GraphAndNetwork, Network, SNP, Software
Version	1.18.1
In Bioconductor since	BioC 3.7 (R-3.5) (5 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	igraph (>= 1.0.1), Matrix, memoise (>= 2.0.0), methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats(>= 1.20.0), stats, utils
LinkingTo	Rcpp, RcppEigen (>= 0.3.3.5.0)
Suggests	biomaRt(>= 2.34.1), circlize (>= 0.4.11), STRINGdb(>= 2.2.0), httr (>= 1.2.1), IRanges(>= 2.8.2), S4Vectors(>= 0.12.2), knitr, testthat, readr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/hclimente/martini
BugReports	https://github.com/hclimente/martini/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	martini_1.18.1.tar.gz
Windows Binary	martini_1.18.1.zip
macOS Binary (x86_64)	martini_1.18.1.tgz
macOS Binary (arm64)	martini_1.18.1.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 3.16	Source Archive