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Run gene set enrichment analysis

Source: R/analysis_enrichment.R
sn_enrich.Rd

Runs GO, KEGG, or MSigDB enrichment using clusterProfiler. It supports both over-representation analysis (ORA) and ranked-list GSEA. The enrichment input can be a gene vector, a ranked numeric vector, a data frame, or a Seurat object paired with source_de_name to reuse stored DE results.

Usage

sn_enrich(
  x,
  gene_clusters = NULL,
  analysis = NULL,
  species = NULL,
  database = "GOBP",
  collection = NULL,
  subcollection = NULL,
  pvalue_cutoff = 0.05,
  store_name = "default",
  source_de_name = NULL,
  return_object = inherits(x, "Seurat"),
  prefix = NULL,
  outdir = NULL
)

Arguments

x

A character vector of genes, a named numeric vector for GSEA, a data frame, or a Seurat object when enriching a stored DE result.

gene_clusters

Optional two-sided formula describing the gene column and the grouping/ranking column. Examples include gene ~ cluster for grouped ORA and gene ~ log2fc for GSEA.

analysis

Optional explicit analysis mode. If omitted, Shennong infers ORA versus GSEA from the input type or the formula RHS column type.

species

One of "human" or "mouse".

database

One or more databases. Supported values include GO/KEGG databases such as "GOBP" and MSigDB collections such as "H", "C2", or "C2:CP:REACTOME".

collection

Optional MSigDB collection used when database = "MSIGDB".

subcollection

Optional MSigDB subcollection used when database = "MSIGDB" or when you want to override the parsed subcollection for a collection-level request such as "C2".

pvalue_cutoff

Raw p-value cutoff used to filter returned enrichment tables after the underlying enrichment call completes.

store_name

Name used when storing the enrichment result on a Seurat object. When multiple databases are requested, the database label is appended automatically unless a vector of names is supplied.

source_de_name

Optional stored DE-result name associated with the enrichment input.

return_object

Logical; when TRUE and a Seurat object is available, return the updated Seurat object instead of raw enrichment results.

prefix

Optional filename prefix when writing results.

outdir

Optional output directory. If supplied, each enrichment result is saved as an .rds file.

Value

A single clusterProfiler result, a named list of results when multiple databases are requested, or a Seurat object when return_object = TRUE.

Examples

if (FALSE) { # \dontrun{
sn_enrich(
  x = c("CD3D", "IL7R", "LTB"),
  species = "human",
  database = c("GOBP", "H")
)
} # }