Run Gene Ontology enrichment on NMF program gene sets

Wrapper function for running GO enrichment analysis on top genes from each NMF program using clusterProfiler. Automatically detects and converts gene ID types (symbols, Ensembl, Entrez) for maximum compatibility.

Usage

runProgramGOEnrichment(
  x,
  nmf_name = "NMF",
  n_genes = 50,
  organism = "human",
  ont = "BP",
  pvalue_cutoff = 0.05,
  qvalue_cutoff = 0.1,
  keyType = "auto"
)

Arguments

x

A SingleCellExperiment object with NMF results

nmf_name

Character, name of NMF result to use (default "NMF")

n_genes

Integer, number of top genes per program (default 50)

organism

Character, organism for GO analysis: "human", "mouse" (default "human")

ont

Character, GO ontology: "BP", "MF", "CC", "ALL" (default "BP")

pvalue_cutoff

Numeric, p-value cutoff for significance (default 0.05)

qvalue_cutoff

Numeric, q-value cutoff for significance (default 0.1)

keyType

Character, gene ID type: "auto" (detect), "SYMBOL", "ENSEMBL", "ENTREZID" (default "auto")

Value

List of clusterProfiler enrichResult objects (one per program)

Examples

 
if (FALSE) { # \dontrun{
sce <- runNMFscape(sce, k = 8)
go_results <- runProgramGOEnrichment(sce, organism = "mouse")
# View results for first program
head(go_results[[1]])
} # }