GatherNetworks {pairkat}R Documentation

Gather pathway information from KEGG through the KEGGREST API.

Description

Takes a SummarizedExperiment and constructs a list with KEGG pathways

Usage

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

Arguments

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

Details

Queries KEGG database for known molecular interactions between included metabolites via the KEGGREST API.

Value

a list object containing the original SummarizedExperiment and igraph network objects

Examples


library(SummarizedExperiment)
data(smokers)
# Query KEGGREST API

networks <- GatherNetworks(SE = smokers, keggID = "kegg_id",
species = "hsa", minPathwaySize = 5)


[Package pairkat version 1.0.0 Index]