runEnrichReactionClass: Enrichment analysis for analyte-reaction class mappings

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

Enrichment analysis for analyte-reaction class mappings

Description

Enrichment analysis for analyte-reaction class mappings

Usage

runEnrichReactionClass(
  analytes,
  humanProtein = TRUE,
  alternative = "less",
  includeRaMPids = FALSE,
  db = RaMP()
)

Arguments

analytes	a vector of analyte ids (genes or metabolites) that need to be searched. ID types accepted: chebi and uniprot
humanProtein	require reactions to have a human protein (enzyme or transporter), default True
alternative	alternative hypothesis test passed on to fisher.test(). Options are two.sided, greater, or less (default is "less")
includeRaMPids	include internal RaMP identifiers (default is "FALSE")
db	a RaMP database object

Value

returns a list of [[1]] EC_Level1Stats, dataframe with columns containing reaction class ID, fisher's p value, user analytes in reaction class, and total analytes in reaction class at the enzyme class level 1 , [[2]] EC_Level2Stats, dataframe with columns containing reaction class ID, fisher's p value, user analytes in reaction class, and total analytes in reaction class at the enzyme class level 2, [[3]] analyteType, a string specifying the type of analyte input into the function ("genes", "metabolites", or "both"), and [[4]] result_type, a string specifying enrichment of reaction classes was performed

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