Identify hub TFs

Identifies hub TFs per module using values of module membership and degree.

Usage

identify_hub_TFs(datExpr, TF.network, MM_thresh = 0.8, degree_thresh = 0.9)

Arguments

datExpr

A matrix of TF activity (TFs as rows and samples as columns).

TF.network

TF network obtained from compute.WTCNA().

MM_thresh

Threshold for module membership (e.g., 0.8).

degree_thresh

Quantile threshold for degree (e.g., 0.9 for top 10%).

TFs with high module membership (r > MM_thresh) and among the top percentage of genes by degree (above degree_thresh quantile) are considered hub TFs.

Value

A list with two elements:

hubGenes

Named list of hub TFs per module

detailedData

Dataframe with module, degree, and membership info

Examples

data("tfs.tuto")
data("network.tuto")

hub_tfs <- identify_hub_TFs(t(tfs.tuto), network.tuto, MM_thresh = 0.8, degree_thresh = 0.9)