clique_sum_permutation: Clique Sum

Description Usage Arguments Details Value Author(s) References

View source: R/clique_sum_permutation.R

Description

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

Usage

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clique_sum_permutation(MODifieR_input, db, n_iterations = 10000,
  clique_significance = 0.01, min_clique_size = 5,
  multiple_cores = T, n_cores = 4, dataset_name = NULL)

Arguments

MODifieR_input

A MODifieR input object produced by one of the create_input functions

db

A clique database created by build_clique_db

n_iterations

Number of iterations to be performed for the permutation based p-value

clique_significance

p-value for cliques to be considered significant

min_clique_size

Minimal size for cliques

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

Details

Clique_sum_permutation finds cliques of at least size min_clique_size that are significantly enriched with DEGs. For every clique size, a null distribution is created using the summed -log 10 p-values. The union of maximal cliques with a summed -log 10 p-value below clique_significance and at least min_deg_in_clique is the final disease module.

Value

clique_sum_permutation returns an object of class "MODifieR_module" with subclass "Clique_Sum_permutation". 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

Author(s)

Dirk de Weerd

References

Gustafsson, M., Edström, M., Gawel, D., Nestor, C. E., Wang, H., Zhang, H., … Benson, M. (2014). Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment. Genome Medicine, 6(2), 17. https://doi.org/10.1186/gm534


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