Infer pathway activity with PROGENy and decoupleR — activity_progeny • bulkMAE

Infer pathway activity with PROGENy and decoupleR

Usage

activity_progeny(
  x,
  experiment,
  assay,
  organism = "human",
  top = 500,
  min_size = 5,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
assay: Assay name or one-based assay index.
organism: Organism accepted by decoupleR::get_progeny().
top: Number of responsive genes retained per pathway.
min_size: Minimum regulon size passed to decoupleR::run_mlm().
...: Additional arguments passed to decoupleR::run_mlm().

Value

The native decoupleR result table.