AssignTFRegulons

Define the set of likely target genes (Regulons) for each transcrition factor

Usage

AssignTFRegulons(
  seurat_obj,
  strategy = "A",
  reg_thresh = 0.01,
  n_tfs = 10,
  n_genes = 50,
  wgcna_name = NULL
)

Arguments

seurat_obj

A Seurat object

strategy

method for defining regulons, "A", "B", or "C". See Details for more info.

reg_thresh

threshold for regulatory score in strategies A, B, and C

n_tfs

for strategy A, the number of top TFs to keep for each gene

n_genes

for strategy B, the number of top target genes to keep for each TF

wgcna_name

name of the WGCNA experiment

Value

seurat_obj with the TF Regulon information added

Details

AssignTFRegulons uses the TF network information from ConstructTFNetwork to define sets of confident TF-gene pairs. A "regulon" is the set of target genes for a given TF, and this function provides three different strategies to define TF regulons. Strategy "A" selects the top TFs for each gene, strategy "B" selects the top genes for each TF, and strategy "C" retains all TF-gene pairs above a certain regulatory score (reg_thresh).