getAnalyteFromPathway: Use fast search algorithm to find all pathways from given...

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

Use fast search algorithm to find all pathways from given analytes

Description

Use fast search algorithm to find all pathways from given analytes

Usage

getAnalyteFromPathway(
  db = RaMP(),
  pathway,
  match = "exact",
  analyte_type = "both",
  max_pathway_size = Inf,
  names_or_ids = "names"
)

Arguments

pathway	a string or a vector of strings that contains pathways of interest
match	type of matching to use, options are "exact" or "fuzzy". The default is "exact".
analyte_type	a string denoting the type of analyte to return ("gene", "metabolite", "both")
max_pathway_size	(default Inf), trims returned results to pathways that have fewer than this number
names_or_ids	are the input pathways input as pathway names or as pathway ids of genes and metabolites

Value

a data.frame that contains all search results

Examples

## Not run: 
# To query one pathway:
myanalytes <- getAnalyteFromPathway2(pathway="sphingolipid metabolism")

# To query multiple pathways:
pkg.globals <- setConnectionToRaMP(dbname="ramp2",username="root",conpass="",host = "localhost")
myanalytes <- getAnalyteFromPathway2(pathway=c("De Novo Triacylglycerol Biosynthesis",
"sphingolipid metabolism"))

## End(Not run)

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