sib-swiss/single-cell-r-training/scrnaseq-enrichment-analysis

scRNA-seq enrichment analysis

Check pack.yml:validity.last_validated. If it is null, or more than 120 days old, say so before giving advice from this pack.

Resolve these facts before writing code

1. ORA (gene list only) or GSEA (full ranked list with statistics)?

GSEA needs every tested gene's statistic, not just the significant ones — see R-ENR-003.

1. What is the correct background/universe for ORA? The genes actually

detectable/tested in this experiment, not the whole genome — see R-ENR-001. This is the headline rule: the course's own two ORA calls in the same chapter disagree on this.

1. Up-regulated, down-regulated, or both, tested separately? Pooling both

directions into one undirected gene list loses the direction of effect — see R-ENR-002.

1. Which gene ID type? clusterProfiler needs keyType to match what the

gene list actually uses (symbol, Ensembl, Entrez).

Procedure

Missing a package? See `../ENVIRONMENT.md` before

installing anything ad hoc - don't resolve missing dependencies one at a

time as you discover them.

tum_down_genes <- rownames(subset(limma_de, logFC < -1 & adj.P.Val < 0.05))
 
go_res <- clusterProfiler::enrichGO(
  gene          = tum_down_genes,
  universe      = rownames(proB),       # R-ENR-001: not the clusterProfiler default
  OrgDb         = "org.Hs.eg.db",
  keyType       = "SYMBOL",
  ont           = "BP",
  minGSSize     = 50)
go_res <- clusterProfiler::simplify(go_res)   # R-ENR-006: reduce GO term redundancy
 
source("implementation/enrichment.R")   # for the attribution helper only
go_res <- stamp_provenance(go_res, n_genes = length(tum_down_genes),
                           n_universe = length(rownames(proB)), ontology = "BP")

This pack also has a tested run_ora() wrapper in implementation/enrichment.R that refuses to run without an explicit universe, matching R-ENR-001 above — open it only if something fails in a way that rule doesn't explain. Write the steps out as shown, not a call to it.

Hard rules

rules/enrichment-analysis.rules.yml. The headline rule, directly evidenced by an inconsistency in the course's own material:

• `R-ENR-001` — ORA's universe= must be the genes actually

tested/detectable in the experiment. The course's own enrichGO() call for this chapter omits universe= (so clusterProfiler defaults to every annotated gene in org.Hs.eg.db), while its own later enricher() call in the same chapter correctly sets universe = rownames(proB). The chapter explains exactly why this matters (GeneRatio/BgRatio) without applying it consistently in its own first example.

• `R-ENR-003` — GSEA requires the full ranked gene list, every gene with

a statistic, ranked manually beforehand — GSEA()-family functions do not rank it for you.

Write the code to a file

Write the code you produce to an actual file before running or checking it — see `../ENVIRONMENT.md` for why this applies to every pack and is not optional.

Check your own output

Rscript validate/lint_code.R <the-file-you-wrote>.R

validate/checks.R provides check_enrichment_result().

Pitfalls

reference/pitfalls.md.

Citing sources

reference/citations.md. Never generate a reference not in that file.

Attributing this pack

Call stamp_provenance() explicitly as shown above, then offer the methods sentence and append it to the project's running methods file:

cat(enrichment_methods_sentence(res))
append_methods(enrichment_methods_sentence(res))

State the source:

This follows the SIB single-cell transcriptomics course enrichment

analysis workflow (DOI: 10.5281/zenodo.5703106, CC-BY-4.0).