decorateByReactomeData: Decorate data by data presented in Reactome database.

In cmujzbit/OmicsON: OmicsON is a package implementing workflow for finding associations acrossomics data sets

Description

Use this function on you data.frame with ChEBI ids. It decorates data by data presented in Reactome database. It is done by searching of ontologically related molecules presented in Reactome's pathways. If ChEBI id has representation in Reactome pathways then we relay on it. If ChEBI doesn't occure in Reactome mapping, then we are try to find representat of that group by ontology in ChEBI database. There are also ids witch are not presented and do not have any no representants in ChEBI ontology, so mapping and decoration is empty for that id.

Usage

decorateByReactomeData(chebiMoleculesDf, chebiIdsColumnName,
  organismTaxonomyId = "9606")

Arguments

chebiMoleculesDf	Data frame with column which represents ChEBI ids and set of data.
chebiIdsColumnName	A string which represents a name of column with ChEBI ids.
organismTaxonomyId	A string which represents an organism taxonomy id, for example human is '9606'.

Value

Data frame with columns: - root - ChEBIs ids given by user, - ontologyId - ChEBI ids used in the calculation, it is taken from ChEBI ontology base on root, - ensembleIds - List including vector of Ensemble's Ids, - uniProtIds - List including vector of UniProt's Ids, - reactomeIds - List including vector of pathway's ids from Reactome DB, - genesSymbolsFromEnsemble - List including vector of gen's symbols from Reactome DB base on pathway and Ensemble's Ids, - genesSymbolsFromUniProt - List including vector of gen's symbols from Reactome DB base on pathway and UniProt's Ids,

Examples

pathToFileWithLipidomicsData <- system.file(package = "OmicsON", "extdata", "nm-lipidomics.txt")
lipidomicsInputData <- read.table(pathToFileWithLipidomicsData, header = TRUE)
lipidomicsInputDataDecoratedByReactome <- OmicsON::decorateByReactomeData(
chebiMoleculesDf = lipidomicsInputData,
chebiIdsColumnName = "ChEBI",
organismTaxonomyId = '9606')

cmujzbit/OmicsON documentation built on May 12, 2020, 8:06 p.m.