get_hubs_grn {BioNERO} | R Documentation

## Get hubs for gene regulatory network

### Description

Get hubs for gene regulatory network

Get hubs for protein-protein interaction network

### Usage

    get_hubs_grn(
      edgelist,
      top_percentile = 0.1,
      top_n = NULL,
      return_degree = FALSE,
      ranked = TRUE
    )

    get_hubs_ppi(
      edgelist,
      top_percentile = 0.1,
      top_n = NULL,
      return_degree = FALSE
    )

### Arguments

`edgelist` | A protein-protein interaction network represented as an edge list.
`top_percentile` | Numeric from 0 to 1 indicating the percentage of proteins with the highest degree to consider hubs. Default: 0.1.
`top_n` | Numeric indicating the number of proteins with the highest degree to consider hubs.
`return_degree` | Logical indicating whether to return a data frame of degree for all proteins. If TRUE, the function will return a list instead of a data frame. Default: FALSE.
`ranked` | Logical indicating whether to treat third column of the edge list (edge weights) as ranked values. Ignored if the edge list only contains 2 columns. Default: TRUE.

### Value

A data frame with gene ID in the first column and out degree in the second column or a list of two data frames with hubs and degree for all genes, respectively.

A data frame with protein ID in the first column and degree in the second column or a list of two data frames with hubs and degree for all genes, respectively.

### Examples

    data(filt.se)
    tfs <- sample(rownames(filt.se), size=50, replace=FALSE)
    grn_list <- grn_combined(filt.se, regulators=tfs, nTrees=2)
    ranked_grn <- grn_average_rank(grn_list)
    # split in only 2 groups for demonstration purposes
    filtered_edges <- grn_filter(ranked_grn, nsplit=2)
    hubs <- get_hubs_grn(filtered_edges)
    ppi_edges <- igraph::get.edgelist(igraph::barabasi.game(n=500, directed=FALSE))
    hubs <- get_hubs_ppi(ppi_edges, return_degree = TRUE)

[Package BioNERO version 1.0.4 Index]