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SharedSelectionMLP<-function(DataMLP=NULL,names=NULL){ #Input=result of DiffGenes.2 and Geneset.intersect
which=list()
table=c()
nmethods=length(DataMLP)
if(is.null(names)){
for(j in 1:length(DataMLP)){
names[j]=paste("Method",j,sep=" ")
}
}
temp1g=c()
temp1p=c()
comps=c()
pvalsg=c()
pvalsp=c()
for (i in 1:nmethods){
temp1g=c(temp1g,length(DataMLP[[i]]$Genes$TopDE$Genes))
temp1p=c(temp1p,length(DataMLP[[i]][[3]]$geneSetDescription))
comps=c(comps,length(DataMLP[[i]]$Compounds$LeadCpds))
names(temp1g)[i]=names[i]
names(temp1p)[i]=names[i]
names(comps)[i]=paste("Ncomps",names[i],i,sep=" ")
if (i==1){
if(!(is.na(DataMLP[[i]])[1]) | !(is.na(DataMLP[[i]])[1])){
sharedcomps=DataMLP[[i]]$Compounds$LeadCpds
sharedgenes=DataMLP[[i]]$Genes$TopDE$Genes
sharedpaths=DataMLP[[i]][[3]]$geneSetDescription
pvalsg=c(pvalsg,DataMLP[[i]]$Genes$TopDE$adj.P.Val)
pvalsp=c(pvalsp,DataMLP[[i]]$mean_geneSetPValue)
nsharedcomps=length(DataMLP[[i]]$Compounds$LeadCpds)
nsharedgenes=length(DataMLP[[i]]$Genes$TopDE$Genes)
nsharedpaths=length(DataMLP[[i]][[3]]$geneSetDescription)
names(nsharedgenes)="nshared"
names(nsharedpaths)="nshared"
names(nsharedcomps)="nsharedcomps"
}
}
else{
sharedcomps=intersect(sharedcomps,DataMLP[[i]]$Compounds$LeadCpds)
sharedgenes=intersect(sharedgenes,DataMLP[[i]]$Genes$TopDE$Genes)
sharedpaths=intersect(sharedpaths,DataMLP[[i]][[3]]$geneSetDescription)
nsharedcomps=length(intersect(sharedcomps,DataMLP[[i]]$Compounds$LeadCpds))
nsharedgenes=length(intersect(sharedgenes,DataMLP[[i]]$Genes$TopDE$Genes))
nsharedpaths=length(intersect(sharedpaths,DataMLP[[i]][[3]]$geneSetDescription))
names(nsharedgenes)="nshared"
names(nsharedpaths)="nshared"
names(nsharedcomps)="nsharedcomps"
}
}
pvalsgenes=list()
meanpvalsgenes=c()
meanpvalspaths=c()
pvalspaths=list()
if(nsharedgenes != 0){
for(c in 1:nmethods){
pvalsg=c()
for(g in sharedgenes){
if(!(is.na(DataMLP[[c]])[1])){
pvalsg=c(pvalsg,DataMLP[[c]]$Genes$TopDE$adj.P.Val[DataMLP[[c]]$Genes$TopDE$Genes==g])
}
}
pvalsgenes[[c]]=pvalsg
names(pvalsgenes)[c]=paste("Method",c,sep=" ")
}
for(g1 in 1:length(sharedgenes)){
pvalstemp=c()
for(c in 1:nmethods){
if(!(is.na(DataMLP[[c]])[1])){
pvalstemp=c(pvalstemp,pvalsgenes[[c]][[g1]])
}
}
meanpvalsgenes=c(meanpvalsgenes,mean(pvalstemp))
}
pvalsgenes[[nmethods+1]]=meanpvalsgenes
names(pvalsgenes)[nmethods+1]="Mean pvals genes"
}
else{pvalsgenes=0}
if(nsharedpaths!=0){
for(c in 1:nmethods){
pvalsp=c()
if(!(is.na(DataMLP[[c]])[1])){
for(p in sharedpaths){
pvalsp=c(pvalsp,DataMLP[[c]][[3]][DataMLP[[c]][[3]]$geneSetDescription==p,5])
}
}
pvalspaths[[c]]=pvalsp
names(pvalspaths)[c]=paste("Method",c,sep=" ")
}
for(p1 in 1:length(sharedpaths)){
pvalstemp1=c()
for(c in 1:nmethods){
if(!(is.na(DataMLP[[c]])[1])){
pvalstemp1=c(pvalstemp1,pvalspaths[[c]][[p1]])
}
}
meanpvalspaths=c(meanpvalspaths,mean(pvalstemp1))
}
pvalspaths[[nmethods+1]]=meanpvalspaths
names(pvalspaths)[nmethods+1]="Mean pvals paths"
}
else{pvalpaths=0}
temp=rbind(cbind(temp1g,temp1p),cbind(nsharedgenes,nsharedpaths),cbind(comps,comps),cbind(nsharedcomps,nsharedcomps))
table=cbind(table,temp)
which[[1]]=list(sharedcomps=sharedcomps,sharedgenes=sharedgenes,pvalsgenes=pvalsgenes,sharedpaths=sharedpaths,pvalspaths=pvalspaths)
#names(which)[1]=paste("Cluster",i,sep=" ")
for (i in 1:length(seq(1,dim(table)[2],2))){
number=seq(1,dim(table)[2],2)[i]
colnames(table)[number]=c("G.Cluster")
colnames(table)[number+1]=c("P.Cluster")
}
ResultShared=list(Table=table,Which=which)
return(ResultShared)
}
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