getReactionClassesForAnalytes: getReactionClassesForAnalytes returns reactions class and EC...

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

getReactionClassesForAnalytes returns reactions class and EC numbers for a collection of input compound ids

Description

getReactionClassesForAnalytes returns reactions class and EC numbers for a collection of input compound ids

Usage

getReactionClassesForAnalytes(
  analytes,
  multiRxnParticipantCount = 1,
  humanProtein = TRUE,
  concatResults = F,
  includeReactionIDs = F,
  useIdMapping = F,
  db = RaMP()
)

Arguments

analytes	list of analyte ids
multiRxnParticipantCount	minimum number of analytes to report a reaction class, default = 1
humanProtein	require reactions to have a human protein (enzyme or transporter), default True
concatResults	returns all reaction class levels in one dataframe rather than a list of 3 dataframes
includeReactionIDs	adds the list of reaction ids for each reaction class
useIdMapping	allows one to fuzzy match input ids to chebi and uniprot to support reaction queries.
db	a RaMP database object

Value

returns a three dataframes of reaction EC class information, one for each EC level

Examples

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

reaction.classes <- getReactionClassesForAnalytes(analytes = analytes.of.interest, db = RaMP())

## End(Not run)

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