get_hub_degree {GWENA} | R Documentation

## 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)

[Package GWENA version 1.2.0 Index]