Run one or more decoupleR methods — activity

This general adapter deliberately exposes both enrichment-style methods (aucell, fgsea, gsva, and ora) and network-aware activity methods (mlm, ulm, viper, wmean, and wsum). With statistics = NULL, decoupleR runs its documented default methods and can calculate a consensus.

Usage

activity_decouple(
  x,
  experiment,
  network,
  assay,
  statistics = NULL,
  method_args = list(NULL),
  consensus = TRUE,
  consensus_statistics = NULL,
  source = "source",
  target = "target",
  mor = NULL,
  min_size = 5,
  include_time = FALSE,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
network: Long-format network or gene-set table.
assay: Assay name or one-based assay index.
statistics: Method names accepted by decoupleR::decouple(), or NULL for its defaults.
method_args: List of method-specific argument lists.
consensus: Calculate a consensus score.
consensus_statistics: Optional decoupleR result-statistic names used for consensus scoring, for example norm_mlm and norm_ulm. NULL preserves the backend default.
source, target: Column names identifying regulators/sets and targets.
mor: Optional column containing signed interaction weights. It is mapped to decoupleR's conventional mor column without discarding the original column.
min_size: Minimum number of targets per source.
include_time: Include execution time in the result.
...: Additional arguments passed to decoupleR::decouple().

Value

The native long-format table returned by decoupleR::decouple().