In hanjunwei-lab/crmSubpathway: Identify cancer-related metabolic subpathways

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(crmSubpathway)

Introduction

The crmSubpathway package is a systematic biological tool to identify cancer-related metabolic subpathways. The main capabilities of this tool are as follows:
1. This function uses the k-clique algorithm to split the metabolic pathways in the KEGG database into metabolic subpathways.
2. A stable metabolic subpathway activity matrix is constructed by GSVA or ssGSEA methods.
3. Cancer-related metabolic subpathways are identified through differential analysis.
4. Visualization

Mining metabolic subpathways

library(graph);
library(RBGL);
library(igraph);
library(XML);
file.path<-paste(system.file(package="crmSubpathway"),"/inst/extdata/",sep="")
file.names<-c("hsa00010.xml","hsa00020.xml")
spwlist<-k_clique(file.path,file.names)

Construct metabolic subpathway activity matrix

library(GSVA)
library(parallel)
# Get the dataset of metabolic subpathways we have processed.
Metspwlist<-get("Metspwlist")
# Get the gene expression profile of the case.
Geneexp<-get("Geneexp")
Spwmatrix<-SubpathwayMatrix(Geneexp,Metspwlist)
head(Spwmatrix)

Identify cancer-related metabolic subpathways

library(limma)
# Get the metabolic subpathway matrix.
Spwmatrix<-get("Spwmatrix")
spwDF<-CalculateDF(Spwmatrix,colnames(Spwmatrix),"cancer","control")

Visualize

library(igraph)
plotNetGraph(spwid="00010_1")

library(pheatmap)
DFspw<-get("DFspw")
plotspwheatmap(DFspw,cluster_rows = TRUE,show.colnames=FALSE)

hanjunwei-lab/crmSubpathway documentation built on Jan. 26, 2021, 8:50 a.m.