Nothing
getTopDiseaseLncRNAs <-
function(pheSeed=NULL,genSeed=NULL,lncSeed=NULL
,candidates=NULL,showTop=30,gamma=0.7,x=1/3,y=1/3,a=1/3,b=1/3,GNet,PNet,LNet,GLNet,PGNet,PLNet){
if(x+y>=1){print("The value of x and y range from [0,1]. The sum of x and y must smaller than 1.");break;};
if(a+b>=1){print("The value of a and b range from [0,1]. The sum of a and b must smaller than 1.");break;};
PNodes<-colnames(PNet) #get("PNodes",envir=envi)
GNodes<-colnames(GNet)#get("GNodes",envir=envi)
LNodes<-colnames(LNet)#get("LNodes",envir=envi)
seeds<-getSeed(pheSeed,genSeed,lncSeed,GNodes,LNodes,PNodes)
newpheSeed<-seeds[[1]]
newlncSeed<-seeds[[2]]
newgenSeed<-seeds[[3]]
pheSeedLength<-length(newpheSeed)
genSeedLength<-length(newgenSeed)
lncSeedLength<-length(newlncSeed)
if(sum(pheSeedLength,genSeedLength,lncSeedLength)==0){print("The seeds you input are not in our network. Error! Please re-enter.");break}
if(is.null(newpheSeed)==TRUE){
pheSeedNodeInf1<-paste("The number of the phenotype seeds you input are: 0")
}else{pheSeedNodeInf1<-paste("The number of the phenotype seeds you input are: " ,length(pheSeed))}
pheSeedNodeInf2<-paste("The number of the phenotype seeds used in prioritizing the candidate lncRNA are: " ,length(newpheSeed))
pheSeedNodeInf3<-paste("The phenotype seeds used in prioritizing the candidate lncRNA are: ",paste(newpheSeed,collapse=";"))
if(is.null(newlncSeed)==TRUE){
lncSeedNodeInf1<-paste("The number of the lncRNA seeds you input are: 0")
}else{lncSeedNodeInf1<-paste("The number of the lncRNA seeds you input are: " ,length(lncSeed))}
lncSeedNodeInf2<-paste("The number of the lncRNA seeds used in prioritizing the candidate lncRNA are: " ,length(newlncSeed))
lncSeedNodeInf3<-paste("The lncRNA seeds used in prioritizing the candidate lncRNA are: ",paste(newlncSeed,collapse=";"))
if(is.null(newgenSeed)==TRUE){
genSeedNodeInf1<-paste("The number of the gene seeds you input are: 0")
}else{genSeedNodeInf1<-paste("The number of the gene seeds you input are: " ,length(genSeed))}
genSeedNodeInf2<-paste("The number of the gene seeds used in prioritizing the candidate lncRNA are: " ,length(newgenSeed))
genSeedNodeInf3<-paste("The gene seeds used in prioritizing the candidate lncRNA are: ",paste(newgenSeed,collapse=";"))
Candidates<-getCandidates(pheSeed=newpheSeed,genSeed=newgenSeed,lncSeed=newlncSeed,candidates=candidates,GNodes=GNodes,LNodes=LNodes,PNodes=PNodes)
if(length(Candidates)==0){print("The candidates you input are not in our network. Error! Please re-enter.");break}
if(is.null(Candidates)==FALSE){
CandidatesInf1<-paste("The number of the candidate lncRNA you input are: " ,length(candidates))
}else{CandidatesInf1<-paste("The number of the candidate lncRNA you input are: " ,0)}
CandidatesInf2<-paste("The number of lncRNA candidates to be prioritized are " ,length(Candidates))
DiseaseInf<-rbind(pheSeedNodeInf1,pheSeedNodeInf2,pheSeedNodeInf3,lncSeedNodeInf1,lncSeedNodeInf2,lncSeedNodeInf3,genSeedNodeInf1,genSeedNodeInf2,genSeedNodeInf3,CandidatesInf1,CandidatesInf2)
DiseaseInf<-unname(DiseaseInf)
print(DiseaseInf)
#write.table(DiseaseInf,"DiseaseInf.txt",row.names=FALSE,col.names=FALSE,quote=FALSE,sep="\t")
Attrist<-getPriList(gamma,x,y,a,b,pheSeed=newpheSeed,genSeed=newgenSeed,lncSeed=newlncSeed,GNet=GNet,PNet=PNet,LNet=LNet,GLNet=GLNet,PGNet=PGNet,PLNet=PLNet)
topLncRNAsID<-c()
topLncRNAsScore<-c()
loci<-which(names(Attrist$AllLncRNAsProbs)%in%Candidates)
if(length(loci)<=showTop)show<-length(loci)
if(length(loci)>showTop)show<-showTop
candidateInf<-Attrist$AllLncRNAsProbs[loci]
orderedCandidateInf<-candidateInf[order(candidateInf,decreasing=TRUE)]
topLncRNAsID<-names(orderedCandidateInf)
topLncRNAsScore<-orderedCandidateInf
Rank<-c(1:length(topLncRNAsID))
#LncRNAInf<-get("LncRNAInf",envir=envi) ##pubchem
#topLncRNAsName<-sapply(topLncRNAsID,function(x){as.character(LncRNAInf[which(LncRNAInf[[1]]%in%x),"LncRNAName"][[1]])})
TopLncRNAInf<-data.frame(Rank,topLncRNAsID,topLncRNAsScore)
#TopLncRNAInf[order(TopLncRNAInf[["Rank"]]),]->TopLncRNAInf1
print(show)
TopLncRNAInf2<-TopLncRNAInf[1:show,]
#write.table(TopLncRNAInf,"TopLncRNAInf.txt",row.names=FALSE,col.names=FALSE,quote=FALSE,sep="\t")
return(TopLncRNAInf2)
}
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