get_hub_degree: Determine hub genes based on degree

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

Determine hub genes based on degree

Description

Remove edges from the graph which value is under weight_th then compute degree of each node (gene). Hub gene are genes whose degree value is above average degree value of the thresholded network.

Usage

get_hub_degree(network, modules = NULL, weight_th = 0.2)

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
weight_th	decimal, weight threshold under or equal to which edges will be removed

Details

GWENA natively build networks using WGCNA. These networks are complete in a graph theory sens, meaning all nodes are connected to each other. Therefore a threshold need to be applied so degree of all nodes isn't the same.

Value

A list of vectors, or single vector of gene names

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_degree(mat)

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