Run GSVA or ssGSEA pathway scoring — run

Scores each gene set in each sample from log2(TPM + 1). Rows sharing a stable Ensembl ID are averaged first. GSVA uses a Gaussian kernel (kcdf = "Gaussian"). Scores are descriptive; no test between groups is run.

Usage

run_gsva(
  study,
  species = "auto",
  collection = "hallmark",
  subcollection = NULL,
  genesets = NULL,
  method = c("gsva", "ssgsea"),
  min_size = 10L,
  max_size = 500L
)

Arguments

study: A rsemflow_study or study path.
species: auto, human, or mouse.
collection: MSigDB collection alias or raw collection code.
subcollection: Optional MSigDB subcollection.
genesets: Optional named list or GMT file.
method: gsva or ssgsea.
min_size: Minimum gene-set size.
max_size: Maximum gene-set size.

Value

A pathway-by-sample data frame with gene-set metadata columns.