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

View source: R/ReturnPathwaysEnrich_InputAnalytes.R

getPathwayFromAnalyteR Documentation

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",
  find_synonym = FALSE,
  NameOrIds = "ids",
  includeRaMPids = FALSE
)

Arguments

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")

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 <- getPathwayFromAnalyteV2(analytes = c("2-hydroxyglutarate", "glutamate"))

## End(Not run)

ncats/RaMP-DB documentation built on May 6, 2022, 1:35 a.m.