Calculate module activity scores — module_scores

Implements the approach from Tirosh et al into bixverse, i.e., the AddModuleScore functionality from Seurat. For each module (gene set), computes the average expression of genes in the set minus the average expression of randomly selected control genes from the same expression bins. Genes are binned based on their average expression across cells to ensure controls are expression-matched.

Usage

module_scores_sc(
  object,
  gs_list,
  n_bins = 24L,
  n_ctrl = 100L,
  seed = 42L,
  streaming = FALSE,
  .verbose = TRUE
)

Arguments

object: SingleCells class.
gs_list: Named list. The elements have the gene identifiers of the respective gene sets.
n_bins: Integer. Number of bins to use. Defaults to 24L.
n_ctrl: Integer. Number of control genes to use per gene for each gene set. Defaults to 100L.
seed: Integer. The random seed.
streaming: Boolean. Shall the cell and gene data be streamed in. Useful for larger data sets.
.verbose: Boolean. Controls the verbosity of the function.

Value

description

References

Tirosh et al, Science (2016)