`load_tf_regulon_dorothea()` is retained only to give a clear migration message. DoRothEA is no longer a cosmosR dependency. For the legacy CARNIVAL workflow, supply a prepared CollecTRI regulon explicitly through the `tf_regulon` argument of `preprocess_COSMOS_*()`. It must contain the columns `tf`, `sign`, and `target`. A cached `decoupleR` CollecTRI table has `source`, `target`, and `mor` columns; convert it with `data.frame(tf = collectri_regulon$source, sign = collectri_regulon$mor, target = collectri_regulon$target)`.
Usage
load_tf_regulon_dorothea(confidence = c("A", "B", "C"))