MS_findMappedNodes: Map gene IDs or metabolite IDs onto the network

In MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Description

This function can be used to find out if a set of genes or metabolites of interest can be mapped onto the network.

Usage

MS_findMappedNodes(nodes, network_table)

Arguments

nodes	character vector containing the IDs of the genes or the metabolites to be mapped onto the network. Remember that Entrez IDs or gene symbols can be transformed into KEGG IDs using the function "MS_convertGene( )".
network_table	three-column matrix where each row represents and edge between two nodes. See function "MS_keggNetwork( )".

Value

A list reporting which genes or metabolites can or cannot be mapped onto the network.

References

Carlson, M. org.Hs.eg.db: Genome wide annotation for Human.R package version >= 3.2.3.

Mark, A., et al.(2014) mygene: Access MyGene.Info_ services. R package version >= 1.6.0.

http://www.kegg.jp/kegg/docs/keggapi.html

Examples

data(MetaboSignal_table)

# Map D-glucose ("cpd:C00031"), taurine ("cpd:C00245"), and aldh ("K00128") onto
# onto the network

MS_findMappedNodes(nodes = c("cpd:C00031","cpd:C00245", "K00128"), MetaboSignal_table)

MetaboSignal documentation built on Nov. 8, 2020, 6 p.m.