runEnrichOntologies: Enrichment analysis for metabolite ontology mappings

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

Enrichment analysis for metabolite ontology mappings

Description

Enrichment analysis for metabolite ontology mappings

Usage

runEnrichOntologies(
  mets,
  namesOrIds = "ids",
  alternative = "less",
  minMets = 2,
  minOntologySize = 5,
  maxOntologySize = 1500,
  includeRaMPids = FALSE,
  backgroundType = "database",
  background = "database",
  db = RaMP()
)

Arguments

mets	a vector of metabolites that need to be searched
namesOrIds	whether input is "names" or "ids" (default is "ids", must be the same for mets and background)
alternative	alternative hypothesis test passed on to fisher.test(). Options are two.sided, greater, or less (default is "less")
minMets	minimum number of mets per pathway (pathways with < minMets mets are filtered out).
minOntologySize	the minimum number of ontology members (genes and metabolites) to include the ontology in the output (default = 5)
maxOntologySize	the maximum number of ontology members (genes and metabolites) to include the ontology in the output (default = 150)
includeRaMPids	whether or not to include RaMP IDs in the output (TRUE/FALSE)
backgroundType	type of background that is input by the user. Options are "database" if user wants all mets from the RaMP database will be used; "file", if user wants to input a file with a list of background mets; "list", if user wants to input a vector of analyte IDs; "biospecimen", if user wants to specify a biospecimen type (e.g. blood, adipose tissue, etc.) and have those biospecimen-specific mets used. For genes, only the "database" option is used.
background	background to be used for Fisher's tests. If parameter 'backgroundType="database"', this parameter is ignored (default="database"); if parameter 'backgroundType= "file"', then 'background' should be a file name (with directory); if 'backgroundType="list"', then 'background' should be a vector of RaMP IDs; if 'backgroundType="biospecimen"' then users should specify one of the following: "Blood", "Adipose tissue", "Heart", "Urine", "Brain", "Liver", "Kidney", "Saliva", and "Feces"
db	a RaMP database object

Value

a dataframe with columns containing pathway ID, fisher's p value, user mets in pathway, and total mets in pathway

Examples

## Not run: 
ontologies.enriched <- runEnrichOntologies(mets = c("hmdb:HMDB0000033","hmdb:HMDB0000052",
"hmdb:HMDB0000094", "hmdb:HMDB0000161","hmdb:HMDB0000168","hmdb:HMDB0000191","hmdb:HMDB0000201",
"chemspider:10026", "hmdb:HMDB0006059", "Chemspider:6405", "CAS:5657-19-2","hmdb:HMDB0002511",
"chemspider:20171375", "CAS:133-32-4","CAS:5746-90-7", "CAS:477251-67-5", "hmdb:HMDB0000695",
"chebi:15934", "CAS:838-07-3", "hmdb:HMDBP00789", "hmdb:HMDBP00283", "hmdb:HMDBP00284",
"hmdb:HMDBP00850"))

## End(Not run)

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