getReactionsForAnalytes: getReactionsForAnalytes returns all associated reactions for...

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

getReactionsForAnalytes returns all associated reactions for a collection of input compound ids

Description

getReactionsForAnalytes returns all associated reactions for a collection of input compound ids

Usage

getReactionsForAnalytes(
  analytes,
  onlyHumanMets = F,
  humanProtein = T,
  includeTransportRxns = T,
  rxnDirs = c("UN"),
  includeRxnURLs = F,
  db = RaMP()
)

Arguments

analytes	list of analytes. chebi and/or uniprot ids are required.
onlyHumanMets	boolean to only return pathways containing only human metabolites (ChEBI ontology) (dev in progress)
humanProtein	boolean to only control pathways catalyzed by a human proteins (having human Uniprot) (dev in progress)
includeTransportRxns	if TRUE, returns metabolic and transport reactions, default is TRUE
rxnDirs	character vector of length > 1, specifying reaction directions to return c("UN", "LR", "RL", "BD", "ALL"), default = c("UN").
includeRxnURLs	if TRUE, urls to Rhea.org will be delivered in the result dataframe for each reaction
db	a RaMP database object

Value

a list of 3 dataframes [[1]] met2rxn, reaction information for all metabolite inputs (chebi), [[2]] prot2rxn, reaction information for all protein inputs (uniprot), and [[3]] metProteinCommonReactions, common reactions found across both metabolite and protein inputs (overlap between met2rxn and prot2rxn)

Examples

## Not run: 
analytes.of.interest <- c('chebi:58115', 'chebi:456215',
 'chebi:58245', 'chebi:58450', 'chebi:17596','uniprot:P30520',
'chebi:16335', 'chebi:16750', 'chebi:172878','uniprot:P22102',
 'chebi:62286', 'chebi:77897', 'uniprot:P30566', 'uniprot:P15531',
'uniprot:P00568', 'uniprot:P23109')

reactionsLists <- getReactionsForAnalytes(analytes = analytes.of.interest,
    includeTransportRxns = T, humanProtein = T, db = rampDB )

## End(Not run)

ncats/RaMP-DB documentation built on June 10, 2025, 10:50 a.m.