get_hub_genes {GWENA} | R Documentation

## 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)

[Package GWENA version 1.4.0 Index]