Package: martini 1.25.0

Hector Climente-Gonzalez

martini: GWAS Incorporating Networks

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.

Authors:Hector Climente-Gonzalez [aut, cre], Chloe-Agathe Azencott [aut]

martini_1.25.0.tar.gz
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martini.pdf |martini.html✨
martini/json (API)

# Install 'martini' in R:
install.packages('martini', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hclimente/martini/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:martini-1.25.0(bioc 3.20)martini-1.24.0(bioc 3.19)

softwaregenomewideassociationsnpgeneticvariabilitygeneticsfeatureextractiongraphandnetworknetworkbioinformaticsgenomicsgwasnetwork-analysissnpssystems-biology

16 exports 4 stars 6.14 score 20 dependencies 29 scripts 183 downloads

Last updated 5 months agofrom:4e7b18c632. Checks:OK: 1 NOTE: 7 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 28 2024
R-4.5-win-x86_64NOTESep 28 2024
R-4.5-linux-x86_64NOTESep 28 2024
R-4.4-win-x86_64NOTESep 28 2024
R-4.4-mac-x86_64ERRORSep 28 2024
R-4.4-mac-aarch64NOTESep 28 2024
R-4.3-win-x86_64NOTESep 28 2024
R-4.3-mac-x86_64NOTESep 28 2024
R-4.3-mac-aarch64NOTESep 28 2024

Exports:get_GI_networkget_GM_networkget_GS_networkldweight_edgesplot_ideogramsconesscones_scones.cvscones.cv_search_conessigmodsigmod_sigmod.cvsigmod.cv_simulate_causal_snpssimulate_phenotype

Dependencies:BiocGenericscachemclicpp11fastmapglueigraphlatticelifecyclemagrittrMatrixmemoisepkgconfigRcppRcppEigenrlangsnpStatssurvivalvctrszlibbioc

Running SConES

Héctor Climente-González

Rendered fromscones_usage.Rmdusingknitr::rmarkdownon Sep 28 2024.

Last update: 2021-03-02
Started: 2017-07-13

Simulating SConES-based phenotypes

Héctor Climente-González

Rendered fromsimulate_phenotype.Rmdusingknitr::rmarkdownon Sep 28 2024.

Last update: 2021-03-02
Started: 2017-07-13