lilikoi.KEGGplot: lilikoi.KEGGplot

In Duuudude/lilikoi2: Metabolomics Personalized Pathway Analysis Tool

Description

Visualizes selected pathways based on their metabolites expression data.

Usage

lilikoi.KEGGplot(
  metamat,
  sampleinfo,
  grouporder,
  pathid = "00250",
  specie = "hsa",
  filesuffix = "GSE16873",
  Metabolite_pathway_table = Metabolite_pathway_table
)

Arguments

metamat	metabolite expression data matrix
sampleinfo	is a vector of sample group, with element names as sample IDs.
grouporder	grouporder is a vector with 2 elements, the first element is the reference group name, like 'Normal', the second one is the experimental group name like 'Cancer'.
pathid	character variable, Pathway ID, usually 5 digits.
specie	character, scientific name of the targeted species.
filesuffix	output file suffix
Metabolite_pathway_table	Metabolites mapping table

Value

Pathview visualization output

Examples

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

metamat <- Metadata[, -1]
sampleinfo <- Metadata$Label
names(sampleinfo) <- rownames(Metadata)
grouporder <- unique(Metadata$Label)
lilikoi.KEGGplot(metamat, sampleinfo, grouporder, pathid = '00250',
  specie = 'hsa',filesuffix = 'GSE16873')

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