## Not run:
#
# #####identify pathways related with metastatic prostate cancer###########
# #example 1
# #get example data
# #### get the metastatic prostate cancer interesting metabolite data set
# risk<-GetExampleData(dataset="prostate")
# #### integrate the global non-equivalence of metabolites and the character of
# #### differential metabolites by the monotonic spline model
# pss<-getPSS(risk)
#
# #identify pathways
# anncpdpre<-identifypathway(risk,pss,pathType="KEGG",method="MPINet",annlim=1,bglim=6)
# #convert ann to data.frame
# result<-printGraph(anncpdpre,pathType="KEGG",method="MPINet")
# #print part of the results to screen
# head(result)
#
# ##write the results to tab delimited file.
# write.table(result,file="result.txt",row.names=FALSE,sep="\t")
#
# result1<-printGraph(anncpdpre,pathType="KEGG",method="MPINet",detail=TRUE)
# ##write the results to tab delimited file.
# write.table(result1,file="result1.txt",row.names=FALSE,sep="\t")
#
#
# #example 2
# #get example data from file
# risk<-read.table(paste(system.file(package="MPINet"),"/localdata/prostate.txt",sep=""),
# header=F,sep="\t","\"")
#
# ####convert the data to a character vector
# risk<-as.character(risk[[1]])
#
# pss<-getPSS(risk)
#
# #identify pathways
# anncpdpre<-identifypathway(risk,pss,pathType="KEGG",method="MPINet",annlim=1,bglim=6)
# #convert ann to data.frame
# result<-printGraph(anncpdpre,pathType="KEGG",method="MPINet")
# #print part of the results to screen
# head(result)
#
# #example 3
# #get example data
# #### get the metastatic prostate cancer interesting metabolite data set
# risk<-GetExampleData(dataset="prostate")
# pss<-getPSS(risk)
#
# #identify dysregulated Reactome and KEGG pathways
# anncpdpre<-identifypathway(risk,pss,pathType=c("KEGG","Reactome"),
# method="MPINet",annlim=1,bglim=6)
# #convert ann to data.frame
# result<-printGraph(anncpdpre,pathType=c("KEGG","Reactome"),method="MPINet")
# #print part of the results to screen
# head(result)
#
#
#
# ## End(Not run)
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