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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/martini.html below:

Bioconductor - martini (development version)

martini

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

GWAS Incorporating Networks

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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")
Details biocViews FeatureExtraction, GeneticVariability, Genetics, GenomeWideAssociation, GraphAndNetwork, Network, SNP, Software Version 1.29.0 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 See More 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.

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