martini

GWAS Incorporating Networks

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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	PDF

Details

biocViews	FeatureExtraction, GeneticVariability, Genetics, GenomeWideAssociation, GraphAndNetwork, Network, SNP, Software
Version	1.20.0
In Bioconductor since	BioC 3.7 (R-3.5) (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
Linking To	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
System Requirements
Enhances
URL	https://github.com/hclimente/martini
Bug Reports	https://github.com/hclimente/martini/issues

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Build Report

Package Archives

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

Source Package	martini_1.20.0.tar.gz
Windows Binary	martini_1.20.0.zip (64-bit only)
macOS Binary (x86_64)	martini_1.20.0.tgz
macOS Binary (arm64)	martini_1.20.0.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