martini

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see martini.

GWAS Incorporating Networks

Bioconductor version: 3.20

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

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

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

Installation

To install this package, start R (version "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FeatureExtraction, GeneticVariability, Genetics, GenomeWideAssociation, GraphAndNetwork, Network, SNP, Software

Version 1.26.0

In Bioconductor since BioC 3.7 (R-3.5) (7 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

Package Archives

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

Source Package martini_1.26.0.tar.gz

Windows Binary (x86_64) martini_1.26.0.zip (64-bit only)

macOS Binary (x86_64) martini_1.26.0.tgz

macOS Binary (arm64) martini_1.26.0.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/

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