Performs an over-representation analysis (ORA) using Fisher's exact test on a list of differentially expressed genes against a set of predefined pathways.
Arguments
- diffexp_result
A data frame of differential expression results, where row names correspond to gene identifiers.
- pathways
A data frame with at least two columns: one indicating pathway names (e.g., 'pathway') and one with gene identifiers.
- id_col
Character. The column name in `pathways` that matches gene identifiers in `diffexp_result`.
- pcutoff
Numeric. Adjusted p-value threshold to filter significant pathways (default = 0.05).
Value
A data frame of enriched pathways with columns:
- Pathway
Name of the enriched pathway
- PValue
Raw p-value from Fisher's exact test
- PAdj
Adjusted p-value (Benjamini-Hochberg)
- GeneRatio
Proportion of input genes found in the pathway
- BgRatio
Proportion of background genes found in the pathway
- Genes
Comma-separated list of matched genes