Fetch Pathway or Transcription Factor Signatures from decoupleR — get_decoupleR

This function retrieves references for Progeny, DoRothEA or CollecTRI from the decoupleR package.

Usage

get_decoupleR_reference(
  method = "progeny",
  organism = "human",
  n_genes = 500,
  confidence = NULL,
  ...
)

method: The computational method to use for obtaining the reference: "progeny", "dorothea" or "collectri
organism: The target organism for the reference signatures ("human", "mouse", etc.).
n_genes: The number of top genes to return for Progeny pathways. Only applicable if method is "progeny".
confidence: A vector of confidence levels (A, B, C, D, E) to filter the transcription factor targets from DoRothEA. Only applicable if method is "dorothea".
...: Additional parameters to fine-tune the method's execution.

A data frame containing the requested reference