getPathwayFromAnalyte: Function that search analytes (gene or compounds) or a list...

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

Function that search analytes (gene or compounds) or a list of analytes and returns associated pathways

Description

Function that search analytes (gene or compounds) or a list of analytes and returns associated pathways

Usage

getPathwayFromAnalyte(
  analytes = "none",
  findSynonym = FALSE,
  namesOrIds = "ids",
  includeRaMPids = FALSE,
  includeSmpdb = FALSE,
  minPathwaySize = 5,
  maxPathwaySize = 150,
  db = RaMP(),
  ...
)

Arguments

analytes	a vector of analytes (genes or metabolites) that need to be searched
findSynonym	find all synonyms or just return same synonym (T/F)
namesOrIds	whether input is "names" or "ids" (default is "ids")
includeRaMPids	include internal RaMP identifiers (default is "FALSE")
includeSmpdb	Include pathways from smpdb/hmdb in analysis. Excluded by default since definitions are highly redundant
minPathwaySize	the minimum number of pathway members (genes and metabolites) to include the pathway in the output (default = 5)
maxPathwaySize	the maximum number of pathway memnbers (genes and metaboltes) to include the pathway in the output (default = 150)
db	a RaMP database object
...	Internal Use - for handling deprecated parameter names

Value

a list contains all metabolites as name and pathway inside.

Examples

## Not run: 
getPathwayFromAnalyte(db = rampDB, namesOrIds="ids", c("ensembl:ENSG00000135679",
     "hmdb:HMDB0000064",
     "hmdb:HMDB0000148",
     "ensembl:ENSG00000141510"))

getPathwayFromAnalyte(db = rampDB, namesOrIds = "names", c("Serotonin", "Bilirubin", "Urea"))

## End(Not run)

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