Run Gene Set Enrichment Analysis on a List of Complexes
Source:R/runEnrichment.R
runComplexEnrichment.RdPerforms enrichment analysis for each complex against a GMT background.
Usage
runComplexEnrichment(
complexList,
gmt,
pAdjustMethod = "Benjamini",
pValueCutoff = 0.05,
verbose = TRUE
)Arguments
- complexList
A named list of protein complexes (character vectors).
- gmt
A named list of gene sets (character vectors).
- pAdjustMethod
Method for multiple testing correction ("Benjamini", "Bonferroni", "FDR"). Defaults to "Benjamini".
- pValueCutoff
Adjusted p-value cutoff. Defaults to 0.05.
- verbose
Logical.
Value
A named list of tibbles. Each tibble contains: - `ID`: Term ID/Name - `Description`: Term Description - `p.adjust`: Adjusted p-value - `Fold`: Fold Enrichment (Observed/Expected) - `TermSize`: Number of genes in the term (Background) - `Count`: Number of genes in the term (Overlap)
Details
**Systems Biology Rationale:** To support the generation of a specific and diverse landscape, this function calculates and returns **Fold Enrichment** and **Term Size** in addition to standard p-values.
- **Fold Enrichment** is used by downstream functions to prioritize specific biological labels over generic ones. - **Term Size** (PopHits) allows you to filter out overly broad terms (e.g., those containing > 10