41 Glossary, function index, and citations

Use this page when the question is “what does this term mean?”, “which function owns this step?”, or “what should I cite and record?”. The task chapters remain the authoritative source for method details and runnable examples.

41.1 Core terms

Term	Meaning in this book
Gene vector	A character vector of selected identifiers used by ORA. It is not a ranked statistic.
Ranked list	A named numeric vector containing the statistic used by GSEA; its names are feature IDs and its order/sign carry direction.
Universe	The features that could have entered the selected ORA list under the study’s detection and filtering process.
ORA	A test for over-representation of a selected set under a defined universe.
GSEA	A test for accumulation of a gene set toward one end of a complete ranking.
`TERM2GENE`	A two-column term-to-gene mapping for custom enrichment.
`TERM2NAME`	An optional mapping from term IDs to readable term names.
`enrichResult`	The standard result object for ordinary enrichment and ORA workflows.
`gseaResult`	The standard result object for GSEA workflows, including enrichment direction and leading-edge information.
`compareClusterResult`	A result object containing comparable enrichment results for multiple groups.
Leading edge / core enrichment	The genes contributing most directly to a GSEA signal.
GSON	A versionable knowledge-resource container; it stores gene sets and metadata, not a new statistical test.
NES	Normalized enrichment score; interpret its sign together with the ranking direction and the gene-set context.
Semantic similarity	A similarity measure between terms, genes, or gene clusters based on ontology or annotation structure.

41.2 Function index by task

Task	Main functions	Output or next step
Prepare identifiers	`bitr()`, `bitr_kegg()`, `select()`, `read.gmt()`	Mapped IDs or custom `TERM2GENE`; inspect mapping loss.
Build GO mappings	`buildGOmap()`	Direct plus ancestor GO annotations for custom enrichment.
Run ORA	`enrichGO()`, `enrichKEGG()`, `enrichPathway()`, `enrichDO()`, `enricher()`	`enrichResult`; continue to result inspection and plots.
Run GSEA	`gseGO()`, `gseKEGG()`, `gsePathway()`, `gseDO()`, `GSEA()`	`gseaResult`; inspect NES, core enrichment, and ranking direction.
Compare groups	`compareCluster()`	`compareClusterResult`; compare clusters with profile plots.
Use network/weighted methods	`nseGO()`, `nseKEGG()`, `nsea()`, `mnsea()`, `ora()`/`gsea()` with `weight =`	Network-aware or weighted result objects; record the extra evidence layer.
Integrate multi-omics	`aggregate_omics()` and related `enrichit` helpers	Aggregated pathway evidence with layer contribution information.
Package knowledge	`gson()`, `gson_GO()`, `gson_KEGG()`, `gson_WP()`, `read.gmt.wp()`	Portable GSON resources that carry source, species, and identifier metadata.
Inspect or subset a resource	`length()`, `names()`, `as.data.frame()`, `x[[i]]`, `x[i]`, `validate_gson()`	A smaller collection with the three mapping tables kept consistent; a report of what the object claims.
Freeze knowledge	`write.gson()`, `read.gson()`, `write.gmt()`	A local copy that reads back identical, or a GMT file for exchange.
Combine knowledge bases	`gsonList()`, `gson_union()`	One result per named source, or one merged membership table.
Trace a gene set to its source	`gson_url()`, `browseGS()`	The web address declared by the object’s `urlpattern`.
Organize terms	`pairwise_termsim()`, `simplify()`, `bayes_enrich()`	Reduced or selected term sets with traceable criteria.
Inspect result objects	`as.data.frame()`, `geneInCategory()`, `setReadable()`	Exportable tables or readable display copies; retain the original object.
Visualize results	`dotplot()`, `barplot()`, `cnetplot()`, `emapplot()`, `treeplot()`, `gseaplot2()`, `hplot()`	Summary, network, semantic, or GSEA figures.
Interpret evidence	`interpret()`, `interpret_agent()`, `interpret_hierarchical()`	Structured draft reports; validate claims against the input evidence.
Preserve the record	`saveRDS()`, `sessionInfo()`, `BiocManager::version()`	Reproducible objects, software context, and provenance.

See the capability map for package-layer ownership and the first workflow for a complete route through several of these functions.

41.3 Citation and version record

For a published or shared analysis, record:

the input file or accession and preprocessing rule;
identifier namespace, mapping summary, selected list, ranked list, and universe;
organism, annotation package, database or GSON source, release, and access date;
the enrichment function, method parameters, correction method, and term filters;
the complete result object, exported tables, figures, and figure-generation code;
package versions, R version, operating system, source commit, and lockfile or environment specification;
the relevant method papers and knowledge-resource citations.

The book bibliography is references.bib. Use citation("clusterProfiler"), citation("enrichplot"), or the relevant package citation for package-specific references. The reproducible report gives a compact record template; the reference appendix provides maintained routes without duplicating this index.