Compute Pathway and Transcription Factor Activities and integrate into SpatialExperiment Using decoupleR

This function computes pathway activities or transcription factor activities using a SpatialExperiment object using various computational methods provided by the decoupleR package.

Usage

compute_activities(
  spe,
  reference,
  method = "wmean",
  assay = "cpm",
  statistic = NULL,
  ...
)

Arguments

spe: The SpatialExperiment object containing spatially resolved expression data.
reference: A reference dataframe, computed using get_decoupleR_reference()
method: The method used to compute activities, such as "wmean", "viper", "gsva", etc. see decoupleR documentation for details.
assay: The name of the assay within the SpatialExperiment to use for calculations.
statistic: In cases where the chosen method produces multiple results, this parameter allows selection of a specific statistic for inclusion in the output.
...: Further arguments passed to the computational methods.

Value

The function returns the input SpatialExperiment object with additional metadata columns representing the computed activities.