martini

This is the development version of martini; for the stable release version, see martini.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

GWAS Incorporating Networks

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-3030-7471 , Chloe-Agathe Azencott [aut] ORCID: 0000-0003-1003-301X

Maintainer: Hector Climente-Gonzalez <hector.climente at a.riken.jp>

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

Hector Climente-Gonzalez, Chloe-Agathe Azencott. martini: GWAS Incorporating Networks. doi:10.18129/B9.bioc.martini, R package version 1.33.0, https://bioconductor.org/packages/martini.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	FeatureExtraction, GeneticVariability, Genetics, GenomeWideAssociation, GraphAndNetwork, Network, SNP, Software
Version	1.33.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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
System Requirements
URL	https://github.com/hclimente/martini
Bug Reports	https://github.com/hclimente/martini/issues

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
Linking To	Rcpp, RcppEigen (>= 0.3.3.5.0)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	martini_1.33.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	martini_1.33.0.tgz
macOS Binary (sonoma-arm64)	martini_1.33.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/martini
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/martini
Package Short Url	https://bioconductor.org/packages/martini/
Package Downloads Report	Download Stats