Calculate single-sample GSEA scores — score_ssgsea • bulkMAE

Uses the current GSVA::ssgseaParam() parameter-object API.

Usage

score_ssgsea(
  x,
  experiment,
  gene_sets,
  assay,
  min_size = 1,
  max_size = Inf,
  normalize = TRUE,
  alpha = 0.25,
  verbose = FALSE,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
gene_sets: Named list of gene sets.
assay: Assay name or one-based assay index.
min_size, max_size: Gene-set size limits.
normalize: Normalize ssGSEA scores by their range.
alpha: Tail-weight exponent used by ssGSEA.
verbose: Show backend progress.
...: Additional arguments passed to GSVA::gsvaParam().

Value

The native matrix-like object returned by GSVA::gsva().