lilikoi.MetaTOpathway: A MetaTOpathway Function

In Duuudude/lilikoi2: Metabolomics Personalized 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

lilikoi.MetaTOpathway(
  q.type,
  hmdb = TRUE,
  pubchem = TRUE,
  chebi = FALSE,
  kegg = TRUE,
  metlin = FALSE
)

Arguments

q.type	The type of the metabolites id such as 'name', 'kegg', 'hmdb','pubchem'
hmdb	if TRUE, match metabolites id to the HMDB database.
pubchem	if TRUE, match metabolites id to the PubChem database.
chebi	if TRUE, match metabolites id to the ChEBI database.
kegg	if TRUE, match metabolites id to the KEGG database.
metlin	if TRUE, match metabolites id to the METLIN database.

Value

A table showing the convertion results from metabolites ids to ids in different metabolomics databases and pathway ids and names.

Examples

dt <- lilikoi.Loaddata(file=system.file("extdata",
  "plasma_breast_cancer.csv", package = "lilikoi"))
Metadata <- dt$Metadata
dataSet <- dt$dataSet
Metabolite_pathway_table=lilikoi.MetaTOpathway('name')

Duuudude/lilikoi2 documentation built on July 22, 2021, 10:59 a.m.