get_hub_genes: Determine hub genes inside each module

In Kumquatum/GWENA: Pipeline for augmented co-expression analysis

Determine hub genes inside each module

Description

Return genes considered as hub genes inside each module of a network following the selected method. Method will be lauched with default parameters. If specific parameters desired, please use directly the function get_hub_... itself.

Usage

get_hub_genes(
  network,
  modules = NULL,
  method = c("highest connectivity", "superior degree", "Kleinberg's score")
)

Arguments

network	matrix or data.frame, square table representing connectivity between each genes as returned by build_net. Can be whole network or a single module.
modules	list, modules defined as list of gene vectors. If null, network is supposed to be the whole network or an already split module
method	string, name of the method to be used for hub gene detection. See details.

Details

highest connectivity

Select the top n (n depending on parameter given) highest connected genes. Similar to WGCNA::chooseTopHubInEachModule.

superior degree

Select genes which degree is greater than average connection degree of the network. Definition from network theory.

Kleinberg's score

Select genes which Kleinberg's score superior to provided threshold.

Value

A list of vectors representing hub genes, by module

Examples

mat <- matrix(runif(40*40), 40)
colnames(mat) <- paste0("gene_", seq_len(ncol(mat)))
rownames(mat) <- paste0("gene_", seq_len(nrow(mat)))
get_hub_genes(mat)

Kumquatum/GWENA documentation built on July 7, 2023, 3:41 p.m.