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Fetch Pathway or Transcription Factor Signatures from decoupleR

get_decoupleR_reference.Rd

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,
  ...
)

Arguments

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.

Value

A data frame containing the requested reference