Performs over‐representation testing via DOSE/clusterProfiler against KEGG or custom gene sets.
Usage
enrich_pathways(
object,
contrasts,
alpha_pathways = 0.1,
pathway_kegg = TRUE,
kegg_organism,
custom_pathways = NULL
)Arguments
- object
A DESeqDataSet or SummarizedExperiment object.
- contrasts
A character vector of contrasts to test. Example:
c("A_vs_B", "C_vs_D").- alpha_pathways
Numeric; p‐value cutoff (default
0.1).- pathway_kegg
Logical; use KEGG pathways if
TRUE.- kegg_organism
KEGG organism code (e.g.
"ppu").- custom_pathways
Data frame with columns
"Pathway"and"Accession", or a GMT file path.