lilikoi.PDSfun: A PDSfun Function

View source: R/lilikoi.PDSfun.r

lilikoi.PDSfunR Documentation

A PDSfun Function

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.

References

Nygård, S., Lingjærde, O.C., Caldas, C. et al. PathTracer: High-sensitivity detection of differential pathway activity in tumours. Sci Rep 9, 16332 (2019). https://doi.org/10.1038/s41598-019-52529-3

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)


lilikoi documentation built on March 18, 2022, 6:06 p.m.