ModuleRegulatoryNetwork: ModuleRegulatoryNetwork

In smorabit/hdWGCNA: hdWGCNA

ModuleRegulatoryNetwork

Description

Summarizes Transcription Factor regulatory networks across co-expression modules.

Usage

ModuleRegulatoryNetwork(seurat_obj, TFs_only = TRUE, wgcna_name = NULL)

Arguments

seurat_obj	A Seurat object containing the single-cell data and WGCNA results.
TFs_only	Logical; if TRUE (default), only transcription factor (TF) genes are included in the regulatory network. If FALSE, the network includes all genes.
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot

Details

This function summarizes transcription factor regulatory networks across modules to infer module-module relationships. The number of directed TF links across modules are counted and normalized. The strength of these links from the XGBoost model are also tracked.

Value

A data frame with the following columns:

source	The source module in the regulatory interaction.
target	The target module in the regulatory interaction.
n_pos	The number of positive regulatory links from the source module to the target module.
sum_pos	The sum of the gain values for the positive links.
n_neg	The number of negative regulatory links from the source module to the target module.
sum_neg	The sum of the gain values for the negative links.
mean_pos	The average gain of the positive links.
mean_neg	The average gain of the negative links.
score_pos	The number of positive links normalized by the number of TFs in the source module.
score_neg	The number of negative links normalized by the number of TFs in the source module.

smorabit/hdWGCNA documentation built on Oct. 23, 2024, 11:19 p.m.