This function merges pathway enrichment results from multiple databases (GO, KEGG, and Reactome) into a single object. The function takes an object of class "functional_module" and various parameters to filter and compute similarity measures.
merge_pathways(
object,
p.adjust.cutoff.go = 0.05,
p.adjust.cutoff.kegg = 0.05,
p.adjust.cutoff.reactome = 0.05,
count.cutoff.go = 5,
count.cutoff.kegg = 5,
count.cutoff.reactome = 5,
sim.cutoff.go = 0.5,
sim.cutoff.kegg = 0.5,
sim.cutoff.reactome = 0.5,
measure.method.go = c("Wang", "Resnik", "Rel", "Jiang", "Lin", "TCSS", "jaccard"),
measure.method.kegg = c("jaccard"),
measure.method.reactome = c("jaccard"),
path = "result",
save_to_local = FALSE
)An object of class "functional_module", typically a result from enrich_pathway function.
Adjusted p-value cutoff for GO database. Default is 0.05.
Adjusted p-value cutoff for KEGG database. Default is 0.05.
Adjusted p-value cutoff for Reactome database. Default is 0.05.
Count cutoff for GO database. Default is 5.
Count cutoff for KEGG database. Default is 5.
Count cutoff for Reactome database. Default is 5.
Similarity cutoff for GO database. Default is 0.5.
Similarity cutoff for KEGG database. Default is 0.5.
Similarity cutoff for Reactome database. Default is 0.5.
A character vector specifying the similarity measure method for GO. Choices are "Wang", "Resnik", "Rel", "Jiang", "Lin", "TCSS", "jaccard". Default is "Wang".
A character vector specifying the similarity measure method for KEGG. Default is "jaccard".
A character vector specifying the similarity measure method for Reactome. Default is "jaccard".
Directory path to save the results. Default is "result".
Logical, if TRUE the results will be saved to local disk.
An object of class "functional_module" with slots for merged pathways from each database.