decorateByStringDbData: Decorate data from previous step (Reactome decoration) by...

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

Description

In this part you search for any extra interactions of gens which you find in Reactome. STRING calls them neighbours. To do it just put results achieved from Reactome decoration step as input to this function.

Usage

decorateByStringDbData(chebiIdsToReactomePathways,
  listOfEnsembleIdColumnName, stringOrganismId = "9606",
  stringDbVersion = "10", idsColumnName = "ontologyId",
  rootColumnName = "root")

Arguments

chebiIdsToReactomePathways	Data frame returned from OmicsON::decorateByReactomeData().
listOfEnsembleIdColumnName	A string which represents a name of column with Ensemble or UniProt ids.
stringOrganismId	A string which represents an organism taxonomy id, for example human is '9606'.
stringDbVersion	String with STRING DB version used to decoration.
idsColumnName	Column name of ChEBI ids from ontology mapping.
rootColumnName	Column name of original ChEBI ids.

Value

Input data frame with presented extra columns: - stringIds - List including vector of all STRING's ids used in computations. - stringGenesSymbolsExpand - List including vector of all neighbours find in STRING database. - stringGenesSymbolsNarrow - List including vector of intersection of all neighbours per id from set of ids used in search.

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')
decoratedByStringBaseOnEnsembleIds <- OmicsON::decorateByStringDbData(
chebiIdsToReactomePathways = lipidomicsInputDataDecoratedByReactome,
listOfEnsembleIdColumnName = 'ensembleIds')

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