CrossReferencing: Various functions for mapping b/w names & database...

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Various functions for mapping b/w names & database identifiers Given a list of compound names or ids, find matched name or ids from selected databases

Description

Given a list of compound names or ids find matched name or IDs from selected databases

Usage

CrossReferencing(
  mSetObj = NA,
  q.type,
  hmdb = T,
  pubchem = T,
  chebi = F,
  kegg = T,
  metlin = F,
  lipid = F
)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects).
q.type	Input the query type, "name" for compound names, "hmdb" for HMDB IDs, "kegg" for KEGG IDs, "pubchem" for PubChem CIDs, "chebi" for ChEBI IDs, "metlin" for METLIN IDs, and "hmdb_kegg" for a both KEGG and HMDB IDs.
hmdb	Logical, T to cross reference to HMDB, F to not.
pubchem	Logical, T to cross reference to PubChem, F to not.
chebi	Logical, T to cross reference to CheBI, F to not.
kegg	Logical, T to cross reference to KEGG, F to not.
metlin	Logical, T to cross reference to MetLin, F to not.
lipid	Logical, if features are lipids (T), a different database will be used for compound matching.

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on Dec. 23, 2024, 3:44 p.m.