rampFastCata: Retrieves analytes that involved in same reaction as input...

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

Retrieves analytes that involved in same reaction as input metabolite

Description

Retrieves analytes that involved in same reaction as input metabolite

Usage

rampFastCata(analytes = "none", namesOrIds = "ids", db = RaMP(), ...)

Arguments

analytes	a vector of analytes that need to be searched
namesOrIds	whether input is "names" or "ids" (default is "ids")
db	a RaMP database object
...	Internal Use - for handling deprecated parameter names

Value

a list of two dataframes containing query results from HMDB and Rhea. If the input is a metabolite, the function will output gene transcript common names and source IDs that are known to catalyze reactions in the same pathway as that metabolite. Conversely, if the input is a gene, the function will return the common name and source id of metabolites known to be catalyzed directly or indirectly by that gene. Input ids and common names will be returned. If no input ids or names are found in the database, the return value will be an empty data frame, 0 rows.

Examples

## Not run: 
inputs.of.interest <- c("kegg:C00186" , "hmdb:HMDB0000148", "kegg:C00780",
 "hmdb:HMDB0000064", "ensembl:ENSG00000115850", "uniprot:Q99259")

new.transcripts <- rampFastCata( analytes = inputs.of.interest, db = rampDB )

## End(Not run)

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