Compute Pathway and Transcription Factor Activities with decoupleR — compute_activities • spacedeconv

Computes pathway or transcription factor activities from a SpatialExperiment using methods provided by the decoupleR package.

Usage

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

Arguments

spe: SpatialExperiment containing expression data.
reference: Reference data frame from get_decoupleR_reference().
method: Activity method (e.g., "wmean", "viper", "gsva"); see decoupleR docs for options.
assay: Assay to use for calculations.
statistic: If multiple statistics are produced, select one to store.
...: Further arguments passed to the selected method.

Value

SpatialExperiment with activity scores added to colData.