GatherNetworks: Gather pathway information from KEGG through the KEGGREST...
In Ghoshlab/pairkat: PaIRKAT

Description Usage Arguments Details Value Examples

View source: R/GatherNetworks.R

Takes a SummarizedExperiment and constructs a list with KEGG pathways

1	GatherNetworks(SE, keggID = "KEGG", species = "hsa", minPathwaySize = 5)

`SE`	A `SummarizedExperiment` with the features of interest in the first `assay`.
`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)