Identify hub TFs

Identifies hub TFs per module using values of module membership and degree. TFs with high module membership (correlation with the module eigengene > MM_thresh) and a degree at or above the degree_thresh quantile of their module are considered hub TFs. The degree of a TF is its intramodular connectivity: the sum of its Pearson correlations with the other TFs of the same module.

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), with TFs in the same order as the module colors of TF.network (e.g. t(TF.network$TFs_matrix)).

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%).

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)