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(
  db = RaMP(),
  analytes = "none",
  find_synonym = FALSE,
  NameOrIds = "ids",
  includeRaMPids = FALSE,
  include_smpdb = FALSE,
  min_path_size = 5,
  max_path_size = 150
)

Arguments

db	a RaMP databse object
analytes	a vector of analytes (genes or metabolites) that need to be searched
find_synonym	find all synonyms or just return same synonym (T/F)
NameOrIds	whether input is "names" or "ids" (default is "ids")
includeRaMPids	include internal RaMP identifiers (default is "FALSE")
include_smpdb	Include pathways from smpdb/hmdb in analysis. Excluded by default since definitions are highly redundant
min_path_size	the minimum number of pathway members (genes and metabolites) to include the pathway in the output (default = 5)
max_path_size	the maximum number of pathway memnbers (genes and metaboltes) to include the pathway in the output (default = 150)

Value

a list contains all metabolites as name and pathway inside.

Examples

## Not run: 
pkg.globals <- setConnectionToRaMP(
  dbname = "ramp2", username = "root",
  conpass = "", host = "localhost"
)
mypath <- getPathwayFromAnalyte(analytes = c("2-hydroxyglutarate", "glutamate"))

## End(Not run)

ncats/RaMP-DB documentation built on June 1, 2024, 9:34 p.m.