lilikoi.PDSfun: A PDSfun Function

In Duuudude/lilikoi2: Metabolomics Personalized Pathway Analysis Tool

Description

This function allows you to compute Pathway Desregulation Score deriving make sure that you have the below database for the metabolites and pathway list: meta_path.RData

Usage

lilikoi.PDSfun(qvec)

Arguments

qvec	This is the Metabolite_pathway_table from MetaTOpathway function. This table includes the metabolites ids and the its corssponding hmdb ids

Value

A large matrix of the pathway deregulation scores for each pathway in different samples.

Examples

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

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