MetaTOpathway: A MetaTOpathway Function

In FADHLyemen/lilikoi_Fadhl: Metabolomics personlaized pathway analysis tool

Description

This function allows you to convert your metabolites id such as names, kegg ids, pubchem ids. into pathways. Metabolites which have not pathways will be excluded from any downstream analysis make sure that you have three database files which are used for exact and fuzzy matching: cmpd_db.rda, syn_nms_db.rda and Sijia_pathway.rda This function was modified version of the name.match function in the below link: https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R

Usage

MetaTOpathway(q.type, hmdb = T, pubchem = T, chebi = F, kegg = T,
  metlin = F)

Arguments

q.type

The type of the metabolites id such as 'name', 'kegg', 'hmdb','pubchem'

Examples

Metabolite_pathway_table=MetaTOpathway('name')
MetaTOpathway()

FADHLyemen/lilikoi_Fadhl documentation built on Aug. 7, 2019, 5:28 a.m.