GatherNetworks {pairkat} | R Documentation |
Takes a SummarizedExperiment
and constructs a list with KEGG pathways
GatherNetworks(SE, keggID = "KEGG", species = "hsa", minPathwaySize = 5)
SE |
A |
keggID |
column name in pathway data containing KEGG IDs |
species |
The three letter KEGG organism ID |
minPathwaySize |
Filter pathways that are below a minimum size |
Queries KEGG database for known molecular interactions between included metabolites via the KEGGREST API.
a list object containing the original SummarizedExperiment and igraph network objects
library(SummarizedExperiment) data(smokers) # Query KEGGREST API networks <- GatherNetworks(SE = smokers, keggID = "kegg_id", species = "hsa", minPathwaySize = 5)