Man pages for martini
GWAS Incorporating Networks

arrange_covarsPrepare covariates for 'scones'
calculateECalculate the environmental component of the phenotype
calculateGCalculate the genetic component of the phenotype
check_installedCheck package is installed
encode_gwasChange encoding of dataset
evoRun evo.
get_evo_settingsGet evo settings.
get_GI_networkGet gene-interaction network.
get_GM_networkGet gene membership network.
get_GS_networkGet genomic sequence network.
get_ppiGet protein-protein interactions.
get_snp_modulesReturn groups of interconnected SNPs.
is_coherentCheck inner coherence of GWAS dataset
ldweight_edgesInclude linkage disequilibrium information in the network.
minigwasDescription of the minigwas dataset.
minippiPPIs for the minigwas dataset.
minisnpMappingGenes for the minigwas dataset.
parse_scones_settingsParse '' settings.
permute_snpMatrixPermute samples
run_sconesRun shake.
sconesFind connected explanatory SNPs.
scones.cvFind connected explanatory SNPs.
score_foldScore the solutions of a k-fold
search_conesFind connected explanatory SNPs.
simulate_causal_snpsSimulate causal SNPs
simulate_phenotypeSimulate phenotype
single_snp_associationCalculate genotype-phhenotype associations
snp2geneMap SNPs to genes.
subnetSubgraph of vertices with an attribute
subvertVertices with an attribute
test_cones_modulesCalculate an empirical p-value for 'find_cones' results.
martini documentation built on Oct. 31, 2019, 10:34 a.m.