Performs fast gene set enrichment analysis (FGSEA) using the `fgseaMultilevel` method,
based on a ranked list of differentially expressed genes and a collection of pathways.
Usage
pathwayFGSEA(diffexp, pathwayCollection)
Arguments
- diffexp
A data frame of differential expression results, with row names as gene IDs
and a `log2FoldChange` column used for ranking genes.
- pathwayCollection
A data frame with at least two columns: one for pathway names (`pathway`)
and one for gene symbols (`gene_symbol`).
Value
A data frame returned by `fgseaMultilevel()`, including columns such as:
- pathway
Name of the pathway
- pval
P-value of enrichment
- padj
Adjusted p-value (FDR)
- ES
Enrichment Score
- NES
Normalized Enrichment Score
- leadingEdge
Vector of leading-edge genes