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Function to calculate sub-components pathway score

gene_set_cc.Rd

The function calculates the score of each pathway connected components

Usage

gene_set_cc(gs_list, gene_network_adj, mc_cores_cc = 2)

Arguments

gs_list

a named list of genes grouped into gene-sets as obtained from `preparing_gs_list`, `preparing_msigdb_list()`, `preparing_DEG_list()` or `preparing_expr_list()` functions

gene_network_adj

adjacency matrix of the whole gene network considered

mc_cores_cc

number of threads to be used for cc calculation

Value

The function returns a list of two object:

  1. membership: results of [igraph::components()] for each pathway considered

  2. pathway_cc: a data frame with

    • pathway: name of the pathway where the components scores are calculated

    • ID: id of the component of the pathway

    • score: component score

    • n_gene: number of genes in the component

    • n_link: number of links in the component

    • gene: names of the genes in the component

Details

By coupling the pathway data to the adjacency matrix, the function identifies the pathway components as connected components (see [igraph::components()] for details). For each component, the function calculates the score as described in the article.

Examples

if (FALSE) {
ptw_list <- list(ptwA = c("A", "B","C"), ptwB = c("D", "E", "F"), ptwC = c("A", "B", "E"))
adj <- matrix(data = sample(c(0,1), 6*6, replace = TRUE), nrow = 6, 
ncol = 6, dimnames = list(LETTERS[1:6], LETTERS[1:6]))
wgt <- rep(1, 6)
p_cc <- pathway_cc(pathway_list = ptw_list, 
gene_network_adj = adj, weight = wgt, mc_cores_cc = 1)
}