Run DoRothEA transcription factor activity inference

Usage

RunDorothea(
  srt,
  assay = NULL,
  layer = "data",
  species = c("Homo_sapiens", "Mus_musculus"),
  confidence = c("A", "B", "C"),
  regulons = NULL,
  method = c("ulm", "viper", "wmean"),
  minsize = 5,
  options = list(),
  assay_name = "dorothea",
  new_assay = TRUE,
  verbose = TRUE
)

Arguments

srt: A Seurat object.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
layer: Assay layer used as the expression matrix.
species: Species used to select bundled DoRothEA regulons.
confidence: DoRothEA confidence levels to keep.
regulons: Optional regulon table with tf, target, mor, and confidence columns. If NULL, bundled dorothea_hs or dorothea_mm data are loaded from the dorothea package.
method: Activity inference backend from decoupleR.
minsize: Minimum regulon size passed to decoupleR.
options: Additional named options passed to the selected decoupleR function.
assay_name: Name of the assay used to store TF activity scores.
new_assay: Whether to store TF activity scores as a new assay.
verbose: Whether to print the message. Default is TRUE.

Value

A Seurat object with DoRothEA results stored in srt@tools[["Dorothea"]].