clique_sum_exact: Clique Sum Exact
In ddeweerd/MODifieRDev: MODifieRDev

Description Usage Arguments Details Value Author(s) References

An implementation of the clique-based disease module inference method proposed by Barrenäs et al.

1
2
3

clique_sum_exact(MODifieR_input, db, clique_significance = 0.01,
  deg_cutoff = 0.05, min_clique_size = 5, min_deg_in_clique = 3,
  multiple_cores = T, n_cores = 4, dataset_name = NULL)

`MODifieR_input`	A MODifieR input object produced by one of the `create_input` functions
`db`	A clique database created by `build_clique_db`
`clique_significance`	p-value for cliques to be considered significant
`deg_cutoff`	p-value cutoff for differentialy expressed genes
`min_clique_size`	Minimal size for cliques
`min_deg_in_clique`	Minimum number of DEGs to be present in a clique
`multiple_cores`	Parallel process using multiple cores?
`n_cores`	Number of cores to use
`dataset_name`	Optional name for the input object that will be stored in the settings object. Default is the variable name of the input object

Clique_sum_exact finds cliques of at least size min_clique_size that are significantly enriched with DEGs. The union of maximal cliques with a Fisher-exact test p-value below clique_significance and at least min_deg_in_clique is the final disease module.

clique_sum_exact returns an object of class "MODifieR_module" with subclass "Clique_Sum_exact". This object is a named list containing the following components:

`module_genes`	A character vector containing the genes in the final module
`settings`	A named list containing the parameters used in generating the object

Dirk de Weerd

Barrenäs F, Chavali S, Alves AC, et al. Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms. Genome Biology. 2012;13(6):R46. doi:10.1186/gb-2012-13-6-r46.

ddeweerd/MODifieRDev documentation built on Nov. 12, 2019, 7:50 a.m.