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Function to calculate cross-talks between pathways of different gene communities

TM_CT.Rd

Calculates cross-talks between pathways composed by gene of different gene communities

Usage

TM_CT(
  gs_list,
  gene_network_adj,
  membership,
  genes,
  weight,
  mc_cores_ct = 2,
  mc_cores_tm = 2
)

Arguments

gs_list

a named list of genes grouped into pathways

gene_network_adj

gene network adjacency matrix

membership

named vector with the membership of `genes` to topological communities. If set to `NULL` the function calculates the communities by using fastgreedy algorithm

genes

vector with the genes of interest to be used for TM-PCT calculation

weight

weights of the genes in `genes`. If not provided, the function assigns to each gene a weight of 1

mc_cores_ct

number of threads to be used to calculate cross talk

mc_cores_tm

number of threads to be used to calcualte TM-PCT on different communities combination

Value

The function returns a list of two object:

  1. comm_pathway_list: the communities pathway lists used for TM-PCT calculation. Each list is named with the name of the gene community

  2. TM_PCT_res: a data frame with

    • commID_1, commID_2: community to which belongs the genes in `pathway_1` and `pathway_2`, respectively

    • pathway_1, pahtway_2: the pathway pair considered

    • score: TM-PCT score

    • ngenes_pathway_1, ngenes_pathway_2: number of genes involved in `pathway_1` and `pathway_2`, respectively

    • n_link: number of links between the pathways considered

    • weight_pathway1, weight_pathway2: cumulative weights of the genes involved in CT in `pathway_1` and `pathway_2`

    • gene_pathway1, gene_pathway2: gene involved in the CT in `pathway_1` and `pathway_2`, respectively

If membership = NULL, then also the membership is returned

Details

The function uses the `membership` data to re-organize the `pathway_list` as to obtain a list of pathway list for each gene community. To do so genes will be grouped into communities and then grouped into pathways. At this point, the function calculates CT between each pathway pairs of different communities that shows at least a link.

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)
 memb <- c(1, 1, 2, 2, 3, 3)
 pct <- TM_PCT(pathway_list = ptw_list, gene_network_adj = adj, weight = wgt, membership = memb, 
                mc_cores_tm = 1, mc_cores_ct = 1)
}