Store an enrichment result on a Seurat object — sn_store

This helper stores enrichment output inside object@misc$enrichment_results[[store_name]] so interpretation and writing helpers can reuse it later.

Usage

sn_store_enrichment(
  object,
  result,
  store_name = "default",
  analysis = c("ora", "gsea"),
  database = "GOBP",
  species = NULL,
  source_de_name = NULL,
  gene_col = "gene",
  score_col = NULL,
  return_object = TRUE
)

Arguments

object: A Seurat object.
result: An enrichment result object or data frame coercible with as.data.frame().
store_name: Name used under object@misc$enrichment_results.
analysis: One of "ora" or "gsea".
database: Database used for enrichment, for example "GOBP".
species: Species label used in the enrichment run.
source_de_name: Optional stored DE result name that produced the input ranked gene list or gene set.
gene_col: Column containing gene symbols when the enrichment input came from a data frame.
score_col: Column containing ranking scores for GSEA inputs.
return_object: If TRUE, return the updated Seurat object.

Value

A Seurat object or a stored-result list.

Examples

if (requireNamespace("Seurat", quietly = TRUE)) {
  counts <- matrix(rpois(10 * 12, lambda = 1), nrow = 10, ncol = 12)
  rownames(counts) <- c(
    "CD3D", "CD3E", "TRAC", "LTB", "MS4A1",
    "CD79A", "HLA-DRA", "LYZ", "ACTB", "MALAT1"
  )
  colnames(counts) <- paste0("cell", 1:12)
  obj <- sn_initialize_seurat_object(counts, species = "human")
  enrich_tbl <- tibble::tibble(
    ID = c("GO:0001", "GO:0002"),
    Description = c("immune response", "lymphocyte activation"),
    NES = c(2.1, 1.7),
    p.adjust = c(0.01, 0.03)
  )
  obj <- sn_store_enrichment(obj, enrich_tbl, store_name = "demo_gsea")
  names(obj@misc$enrichment_results)
}
#> INFO [2026-03-26 18:52:41] Initializing Seurat object for project: Shennong.
#> INFO [2026-03-26 18:52:41] Running QC metrics for human.
#> INFO [2026-03-26 18:52:41] Seurat object initialization complete.
#> [1] "demo_gsea"