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R/identifypathway.R
In MPINet: The package can implement the network-based metabolite pathway identification of pathways.
Defines functions
identifypathway
fdr.est
printGraph
Documented in
fdr.est
identifypathway
printGraph
identifypathway<-function(componentList,PSS,pathType="KEGG",method="MPINet",
weightnum=6,backgroundcid=Getenvir("getBackground"),annlim=1,bglim=6,order="pvalue",decreasing=FALSE){
Veg<-Getenvir("getnodeseq")
pathType<-unique(pathType)
if((length(pathType)==1)&(length(pathType[which(pathType=="KEGG")])>0))
{
pathList<-Getenvir("getpathList('KEGG')")
if(method=="MPINet")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
compoundListinnet<-intersect(Veg,componentList)
message(c("your input componentList have ",length(compoundListinnet)," components in network"))
annList<-list()
N<-length(unique(backgroundcid)) ###number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayId=character(),pathwayName="not known",annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1,
InWeight=0,weight=1,anncompinNetworkNum=0,anncompinNetworkList=character(),riskcompinNetworkNum=0,riskcompinNetworkList=character())
ann$pathwayId<-pathList[i,1] ###pathwayId
ann$pathwayName<-pathList[i,2]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"annBgComponentList"],';')[[1]]####all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
#######################################calcualte the anncompinNetworkNum,anncompinNetworkList,riskcompinNetworkNum,riskcompinNetworkList of pathway i ##########################
inter_2<-intersect(unique(inter),Veg)######## differential metabolites annotate in pathway i and network
riskinnet<-intersect(componentList,Veg)#######differential metabolites in network
ann$anncompinNetworkNum<-length(inter_2) ###anncompinNetworkNum
ann$anncompinNetworkList<-inter_2 ###anncompinNetworkList
ann$riskcompinNetworkNum<-length(riskinnet) ###riskcompinNetworkNum
ann$riskcompinNetworkList<-riskinnet ###riskcompinNetworkList
#######################calculate pathway Inweight################
strinner<-0
metaboliteinpath<-as.character(unlist(tpathmetabolite))
metapathinnet<-intersect(Veg,unlist(tpathmetabolite))
if(length(metapathinnet)>0)
{
pathw<-sum(PSS[metapathinnet,"pss"])
strinner<-pathw/length(metaboliteinpath)
}
ann$InWeight<-strinner ###InWeight
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
#######################calculate pathway weight################
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
InWeightList<-c()
for(j in (1:length(annList)))
{
InWeightList<-c(InWeightList,annList[[j]]$InWeight)
}
meanweight<-mean(InWeightList)
for(j in (1:length(annList)))
{
w<-annList[[j]]$InWeight/meanweight
annList[[j]]$weight<-w^weightnum
}
############################### calculate Pvalue###########################
for(i in (1:length(annList)))
{
tv<-as.numeric(annList[[i]]["weight"])
if(tv>0)
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),tv,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}
}####### for(i in (1:length(annList)))
}###########if(length(annList)>0)
}###############if(length(annList)>0)
}####if(length(pathList[,1])>0)
}#####if method=="MPINet"
if(method=="Hyper")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
annList<-list()
N<-length(unique(backgroundcid)) ### number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayId=character(),pathwayName="not known",annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1)
ann$pathwayId<-pathList[i,1] ###pathwayId
ann$pathwayName<-pathList[i,2]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"annBgComponentList"],';')[[1]]####all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
###############################calculate Pvalue###########################
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
for(i in (1:length(annList)))
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),1,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}####### for(i in (1:length(annList)))
}########if(length(annList)>0)
}########if(length(annList)>0)
}####if(length(pathList[,1])>0)
}######if method=="Hyper"
}############# if (pathtype=="KEGG")
else
{
if((length(pathType)==1)&(length(pathType[which(pathType=="consensusPath")])>0))
{
pathList<-Getenvir("consensusPath")
}
else
{
pathListall<-Getenvir("consensusPath")
pathList<-pathListall[which(as.character(pathListall[,2])%in%pathType),]
}
if(method=="MPINet")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
compoundListinnet<-intersect(Veg,componentList)
message(c("your input componentList have ",length(compoundListinnet)," components in network"))
annList<-list()
N<-length(unique(backgroundcid)) ###number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayName="not known",pathsource=character(),annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1,
InWeight=0,weight=1,anncompinNetworkNum=0,anncompinNetworkList=character(),riskcompinNetworkNum=0,riskcompinNetworkList=character())
ann$pathsource<-pathList[i,2] ###pathwayId
ann$pathwayName<-pathList[i,1]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"metabolites"],';')[[1]]####all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
#######################################calculate anncompinNetworkNum,anncompinNetworkList,riskcompinNetworkNum,riskcompinNetworkList of pathway i##########################
inter_2<-intersect(unique(inter),Veg)########differential metabolites annotate in pathway i and network
riskinnet<-intersect(componentList,Veg)#######differential metabolites in network
ann$anncompinNetworkNum<-length(inter_2) ###anncompinNetworkNum
ann$anncompinNetworkList<-inter_2 ###anncompinNetworkList
ann$riskcompinNetworkNum<-length(riskinnet) ###riskcompinNetworkNum
ann$riskcompinNetworkList<-riskinnet ###riskcompinNetworkList
#######################calculate pathway InWeigtht################
strinner<-0
metaboliteinpath<-as.character(unlist(tpathmetabolite))
metapathinnet<-intersect(Veg,unlist(tpathmetabolite))
if(length(metapathinnet)>0)
{
pathw<-sum(PSS[metapathinnet,"pss"])
strinner<-pathw/length(metaboliteinpath)
}
ann$InWeight<-strinner ###InWeight
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
InWeightList<-c()
for(j in (1:length(annList)))
{
InWeightList<-c(InWeightList,annList[[j]]$InWeight)
}
meanweight<-mean(InWeightList)
for(j in (1:length(annList)))
{
w<-annList[[j]]$InWeight/meanweight
annList[[j]]$weight<-w^weightnum
}
###############################calculate Pvalue###########################
for(i in (1:length(annList)))
{
tv<-as.numeric(annList[[i]]["weight"])
if(tv>0)
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),tv,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}
}####### for(i in (1:length(annList)))
}########if(length(annList)>0)
}########if(length(annList)>0)
}####if(length(pathList[,1])>0)
}#####if method=="MPINet"
if(method=="Hyper")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
annList<-list()
N<-length(unique(backgroundcid)) ###number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayName="not known",pathsource=character(),annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1)
ann$pathsource<-pathList[i,2] ###pathwayId
ann$pathwayName<-pathList[i,1]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"metabolites"],';')[[1]]#### all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
###############################calculate Pvalue###########################
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
for(i in (1:length(annList)))
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),1,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}####### for(i in (1:length(annList)))
}###########if(length(annList)>0)
}####if(length(annList)>0)
}####if(length(pathList[,1])>0)
}######if method=="Hyper"
}###########else
###############################calculate fdr#####################################
if(length(annList)>0)
{
p_value<-sapply(annList,function(x) return(x$pvalue))
#fdrtool.List<-fdrtool(p_value,statistic="pvalue",plot=FALSE,verbose=FALSE)
#print(fdrtool.List$qval)
#for(i in seq(annList)){
# annList[[i]]$qvalue<-fdrtool.List$qval[i]
# annList[[i]]$lfdr<-fdrtool.List$lfdr[i]
#}
fdr.List<-fdr.est(p_value)
for(i in seq(annList))
{
annList[[i]]$fdr<-fdr.List[i]
}
#names(annList)<-sapply(graphList,function(x) x$number)
annList<-annList[order(sapply(annList,function(x) x[[order]]),decreasing=decreasing)]
}
return(annList)
}######function identifypathway
#####################################################################
fdr.est<-function(p)
{
m <- length(ind <- which(!is.na(p)))
fdr <- rep(NA, length(p))
stat <- cbind(1:length(p), p, fdr)
stat[ind, 3] <- unlist(lapply(stat[ind, 2], function(x) {
c <- length(which(stat[ind, 2] <= x))
m * x/c
}))
stat[ind, ] <- stat[ind, ][order(stat[, 2], decreasing = TRUE),
]
stat[ind, 3] <- cummin(stat[ind, 3])
fdr <- stat[order(stat[, 1]), 3]
fdr[which(fdr > 1)] <- 1
return(fdr)
}
#####################################################################
printGraph<-function(ann,detail=FALSE,method="MPINet",pathType="KEGG")
{
pathType<-unique(pathType)
if((length(pathType)==1)&(length(pathType[which(pathType=="KEGG")])>0)){
if(method=="MPINet")
{
if(detail==FALSE)
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
fdr<-sapply(ann,function(x) x$fdr)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
#anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
weight<-sapply(ann,function(x) x$weight)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
# fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE,
annComponentinNetRatio=annComponentinNetRatio)
}
else
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
weight<-sapply(ann,function(x) x$weight)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,
annComponentinNetRatio=annComponentinNetRatio,anncompinNetworkList=anncompinNetworkList,riskcompinNetworkList=riskcompinNetworkList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
}############if method="MPINet"
if(method=="Hyper")
{
if(detail==FALSE)
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
fdr<-sapply(ann,function(x) x$fdr)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
#anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
# annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
# Tw<-sapply(ann,function(x) x$Tw)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE)
}
else
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
#annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
#riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
#Tw<-sapply(ann,function(x) x$Tw)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
} ########if(method=="Hyper")
}######if (pathType=="KEGG")
else
{
if(method=="MPINet")
{
if(detail==FALSE)
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
#anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
weight<-sapply(ann,function(x) x$weight)
fdr<-sapply(ann,function(x) x$fdr)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
# fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr))
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE,
annComponentinNetRatio=annComponentinNetRatio)
}
else
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
weight<-sapply(ann,function(x) x$weight)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,annComponentinNetRatio=annComponentinNetRatio,
anncompinNetworkList=anncompinNetworkList,riskcompinNetworkList=riskcompinNetworkList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
}############if method="MPINet"
if(method=="Hyper")
{
if(detail==FALSE)
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
fdr<-sapply(ann,function(x) x$fdr)
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE)
}
else
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
#annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
#riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
#Tw<-sapply(ann,function(x) x$Tw)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
} ########if(method=="Hyper")
}###########else
}##########printGraph
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Defines functions identifypathway fdr.est printGraph
Documented in fdr.est identifypathway printGraph
identifypathway<-function(componentList,PSS,pathType="KEGG",method="MPINet",
weightnum=6,backgroundcid=Getenvir("getBackground"),annlim=1,bglim=6,order="pvalue",decreasing=FALSE){
Veg<-Getenvir("getnodeseq")
pathType<-unique(pathType)
if((length(pathType)==1)&(length(pathType[which(pathType=="KEGG")])>0))
{
pathList<-Getenvir("getpathList('KEGG')")
if(method=="MPINet")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
compoundListinnet<-intersect(Veg,componentList)
message(c("your input componentList have ",length(compoundListinnet)," components in network"))
annList<-list()
N<-length(unique(backgroundcid)) ###number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayId=character(),pathwayName="not known",annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1,
InWeight=0,weight=1,anncompinNetworkNum=0,anncompinNetworkList=character(),riskcompinNetworkNum=0,riskcompinNetworkList=character())
ann$pathwayId<-pathList[i,1] ###pathwayId
ann$pathwayName<-pathList[i,2]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"annBgComponentList"],';')[[1]]####all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
#######################################calcualte the anncompinNetworkNum,anncompinNetworkList,riskcompinNetworkNum,riskcompinNetworkList of pathway i ##########################
inter_2<-intersect(unique(inter),Veg)######## differential metabolites annotate in pathway i and network
riskinnet<-intersect(componentList,Veg)#######differential metabolites in network
ann$anncompinNetworkNum<-length(inter_2) ###anncompinNetworkNum
ann$anncompinNetworkList<-inter_2 ###anncompinNetworkList
ann$riskcompinNetworkNum<-length(riskinnet) ###riskcompinNetworkNum
ann$riskcompinNetworkList<-riskinnet ###riskcompinNetworkList
#######################calculate pathway Inweight################
strinner<-0
metaboliteinpath<-as.character(unlist(tpathmetabolite))
metapathinnet<-intersect(Veg,unlist(tpathmetabolite))
if(length(metapathinnet)>0)
{
pathw<-sum(PSS[metapathinnet,"pss"])
strinner<-pathw/length(metaboliteinpath)
}
ann$InWeight<-strinner ###InWeight
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
#######################calculate pathway weight################
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
InWeightList<-c()
for(j in (1:length(annList)))
{
InWeightList<-c(InWeightList,annList[[j]]$InWeight)
}
meanweight<-mean(InWeightList)
for(j in (1:length(annList)))
{
w<-annList[[j]]$InWeight/meanweight
annList[[j]]$weight<-w^weightnum
}
############################### calculate Pvalue###########################
for(i in (1:length(annList)))
{
tv<-as.numeric(annList[[i]]["weight"])
if(tv>0)
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),tv,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}
}####### for(i in (1:length(annList)))
}###########if(length(annList)>0)
}###############if(length(annList)>0)
}####if(length(pathList[,1])>0)
}#####if method=="MPINet"
if(method=="Hyper")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
annList<-list()
N<-length(unique(backgroundcid)) ### number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayId=character(),pathwayName="not known",annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1)
ann$pathwayId<-pathList[i,1] ###pathwayId
ann$pathwayName<-pathList[i,2]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"annBgComponentList"],';')[[1]]####all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
###############################calculate Pvalue###########################
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
for(i in (1:length(annList)))
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),1,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}####### for(i in (1:length(annList)))
}########if(length(annList)>0)
}########if(length(annList)>0)
}####if(length(pathList[,1])>0)
}######if method=="Hyper"
}############# if (pathtype=="KEGG")
else
{
if((length(pathType)==1)&(length(pathType[which(pathType=="consensusPath")])>0))
{
pathList<-Getenvir("consensusPath")
}
else
{
pathListall<-Getenvir("consensusPath")
pathList<-pathListall[which(as.character(pathListall[,2])%in%pathType),]
}
if(method=="MPINet")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
compoundListinnet<-intersect(Veg,componentList)
message(c("your input componentList have ",length(compoundListinnet)," components in network"))
annList<-list()
N<-length(unique(backgroundcid)) ###number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayName="not known",pathsource=character(),annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1,
InWeight=0,weight=1,anncompinNetworkNum=0,anncompinNetworkList=character(),riskcompinNetworkNum=0,riskcompinNetworkList=character())
ann$pathsource<-pathList[i,2] ###pathwayId
ann$pathwayName<-pathList[i,1]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"metabolites"],';')[[1]]####all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
#######################################calculate anncompinNetworkNum,anncompinNetworkList,riskcompinNetworkNum,riskcompinNetworkList of pathway i##########################
inter_2<-intersect(unique(inter),Veg)########differential metabolites annotate in pathway i and network
riskinnet<-intersect(componentList,Veg)#######differential metabolites in network
ann$anncompinNetworkNum<-length(inter_2) ###anncompinNetworkNum
ann$anncompinNetworkList<-inter_2 ###anncompinNetworkList
ann$riskcompinNetworkNum<-length(riskinnet) ###riskcompinNetworkNum
ann$riskcompinNetworkList<-riskinnet ###riskcompinNetworkList
#######################calculate pathway InWeigtht################
strinner<-0
metaboliteinpath<-as.character(unlist(tpathmetabolite))
metapathinnet<-intersect(Veg,unlist(tpathmetabolite))
if(length(metapathinnet)>0)
{
pathw<-sum(PSS[metapathinnet,"pss"])
strinner<-pathw/length(metaboliteinpath)
}
ann$InWeight<-strinner ###InWeight
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
InWeightList<-c()
for(j in (1:length(annList)))
{
InWeightList<-c(InWeightList,annList[[j]]$InWeight)
}
meanweight<-mean(InWeightList)
for(j in (1:length(annList)))
{
w<-annList[[j]]$InWeight/meanweight
annList[[j]]$weight<-w^weightnum
}
###############################calculate Pvalue###########################
for(i in (1:length(annList)))
{
tv<-as.numeric(annList[[i]]["weight"])
if(tv>0)
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),tv,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}
}####### for(i in (1:length(annList)))
}########if(length(annList)>0)
}########if(length(annList)>0)
}####if(length(pathList[,1])>0)
}#####if method=="MPINet"
if(method=="Hyper")
{
componentList<-unique(intersect(componentList,backgroundcid))
message(c("your input componentList have ",length(componentList)," components in background"))
annList<-list()
N<-length(unique(backgroundcid)) ###number of background compounds
if(length(pathList[,1])>0)
{
for(i in 1:length(pathList[,1]))
{
ann<-list(pathwayName="not known",pathsource=character(),annComponentList=character(),annComponentNumber=0,
annBgComponentList=character(),annBgNumber=0,componentNumber=0,bgNumber=0,pvalue=1,fdr=1)
ann$pathsource<-pathList[i,2] ###pathwayId
ann$pathwayName<-pathList[i,1]###pathwayName
ann$annBgComponentList<-pathList[i,3]###annBgComponentList
ann$bgNumber<-N ### bgNumber
ann$componentNumber<-length(componentList) ###componentNumber
tpathmetabolite<-strsplit(pathList[i,"metabolites"],';')[[1]]#### all metabolites in pathway i
m1<-length(unique(unlist(tpathmetabolite)))
inter<-unique(intersect(as.character(componentList),unlist(tpathmetabolite)))
x<-length(unique(inter))
ann$annBgNumber<-m1 ####annBgNumber
ann$annComponentNumber<-x ####annComponentNumber
ann$annComponentList<-inter ####annComponentList
annList[[i]]<-ann
}#####for i in 1:length(pathList[,1])
###############################calculate Pvalue###########################
annList<-annList[sapply(annList,function(x) x$annComponentNumber>(annlim-1))]
if(length(annList)>0)
{
annList<-annList[sapply(annList,function(x) x$annBgNumber>(bglim-1))]
if(length(annList)>0)
{
for(i in (1:length(annList)))
{
pvalue<- pWNCHypergeo((as.numeric(annList[[i]]["annComponentNumber"])-1),as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["bgNumber"])-as.numeric(annList[[i]]["annBgNumber"]),as.numeric(annList[[i]]["componentNumber"]),1,precision=1E-100,lower.tail=FALSE)
annList[[i]]["pvalue"]<-pvalue
}####### for(i in (1:length(annList)))
}###########if(length(annList)>0)
}####if(length(annList)>0)
}####if(length(pathList[,1])>0)
}######if method=="Hyper"
}###########else
###############################calculate fdr#####################################
if(length(annList)>0)
{
p_value<-sapply(annList,function(x) return(x$pvalue))
#fdrtool.List<-fdrtool(p_value,statistic="pvalue",plot=FALSE,verbose=FALSE)
#print(fdrtool.List$qval)
#for(i in seq(annList)){
# annList[[i]]$qvalue<-fdrtool.List$qval[i]
# annList[[i]]$lfdr<-fdrtool.List$lfdr[i]
#}
fdr.List<-fdr.est(p_value)
for(i in seq(annList))
{
annList[[i]]$fdr<-fdr.List[i]
}
#names(annList)<-sapply(graphList,function(x) x$number)
annList<-annList[order(sapply(annList,function(x) x[[order]]),decreasing=decreasing)]
}
return(annList)
}######function identifypathway
#####################################################################
fdr.est<-function(p)
{
m <- length(ind <- which(!is.na(p)))
fdr <- rep(NA, length(p))
stat <- cbind(1:length(p), p, fdr)
stat[ind, 3] <- unlist(lapply(stat[ind, 2], function(x) {
c <- length(which(stat[ind, 2] <= x))
m * x/c
}))
stat[ind, ] <- stat[ind, ][order(stat[, 2], decreasing = TRUE),
]
stat[ind, 3] <- cummin(stat[ind, 3])
fdr <- stat[order(stat[, 1]), 3]
fdr[which(fdr > 1)] <- 1
return(fdr)
}
#####################################################################
printGraph<-function(ann,detail=FALSE,method="MPINet",pathType="KEGG")
{
pathType<-unique(pathType)
if((length(pathType)==1)&(length(pathType[which(pathType=="KEGG")])>0)){
if(method=="MPINet")
{
if(detail==FALSE)
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
fdr<-sapply(ann,function(x) x$fdr)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
#anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
weight<-sapply(ann,function(x) x$weight)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
# fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE,
annComponentinNetRatio=annComponentinNetRatio)
}
else
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
weight<-sapply(ann,function(x) x$weight)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,
annComponentinNetRatio=annComponentinNetRatio,anncompinNetworkList=anncompinNetworkList,riskcompinNetworkList=riskcompinNetworkList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
}############if method="MPINet"
if(method=="Hyper")
{
if(detail==FALSE)
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
fdr<-sapply(ann,function(x) x$fdr)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
#anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
# annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
# Tw<-sapply(ann,function(x) x$Tw)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE)
}
else
{
pathwayId<-sapply(ann,function(x) x$pathwayId)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
#annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
#riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
#Tw<-sapply(ann,function(x) x$Tw)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
} ########if(method=="Hyper")
}######if (pathType=="KEGG")
else
{
if(method=="MPINet")
{
if(detail==FALSE)
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
#anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
weight<-sapply(ann,function(x) x$weight)
fdr<-sapply(ann,function(x) x$fdr)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
# fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr))
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE,
annComponentinNetRatio=annComponentinNetRatio)
}
else
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
weight<-sapply(ann,function(x) x$weight)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,weight=weight,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,annComponentinNetRatio=annComponentinNetRatio,
anncompinNetworkList=anncompinNetworkList,riskcompinNetworkList=riskcompinNetworkList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
}############if method="MPINet"
if(method=="Hyper")
{
if(detail==FALSE)
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
fdr<-sapply(ann,function(x) x$fdr)
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE)
}
else
{
pathsource<-sapply(ann,function(x) x$pathsource)
pathwayName<-sapply(ann,function(x) x$pathwayName)
annComponentList<-sapply(ann, function(x){ paste(x$annComponentList,collapse=";") })
annBgComponentList<-sapply(ann, function(x) x$annBgComponentList)#######
annComponentRatio<-sapply(ann,function(x) paste(x$annComponentNumber,x$componentNumber,sep="/"))
annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
pvalue<-sapply(ann,function(x) x$pvalue)
#InWeight<-sapply(ann,function(x) x$InWeight)
#OutWeight<-sapply(ann,function(x) x$OutWeight)
#AllWeight<-sapply(ann,function(x) x$AllWeight)
# anncompinNetworkNum<-sapply(ann,function(x) x$anncompinNetworkNum)
#anncompinNetworkList<-sapply(ann, function(x){ paste(x$anncompinNetworkList,collapse=";") })
#riskcompinNetworkNum<-sapply(ann,function(x) x$riskcompinNetworkNum)
#annComponentinNetRatio<-sapply(ann,function(x) paste(x$anncompinNetworkNum,x$riskcompinNetworkNum,sep="/"))
#riskcompinNetworkList<-sapply(ann, function(x){ paste(x$riskcompinNetworkList,collapse=";") })
#Tw<-sapply(ann,function(x) x$Tw)
#qvalue<-sapply(ann,function(x) x$qvalue)
#lfdr<-sapply(ann,function(x) x$lfdr)
fdr<-sapply(ann,function(x) x$fdr)
#ann.data.frame<-as.data.frame(cbind(pathwayId,pathwayName,annComponentRatio,
# annBgRatio,pvalue,qvalue,lfdr,annComponentList,annBgComponentList))
ann.data.frame<-data.frame(pathwayName=pathwayName,pathsource=pathsource,annComponentRatio=annComponentRatio,
annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,annComponentList=annComponentList,
annBgComponentList=annBgComponentList,stringsAsFactors=FALSE)
}
return(ann.data.frame)
} ########if(method=="Hyper")
}###########else
}##########printGraph
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