Nothing
PreparePathway<-function(Object,GeneExpr,topG,sign){
FoundGenes=NULL
FoundComps=NULL
FoundGenes=FindElement("Genes",Object)
if(is.null(FoundGenes)|(is.list(FoundGenes) & length(FoundGenes) == 0)){
FoundComps=FindElement("Compounds",Object)
if(is.null(FoundComps)|(is.list(FoundComps) & length(FoundComps) == 0)){
stop("Specify either the p-values of the genes or a selection of compounds to test for DE genes.")
}
pvalsgenes=list()
FoundGenes=list()
CompsP=list()
TopDEP=list()
for(i in 1:length(FoundComps)){
LeadCpds=FoundComps[[i]]$LeadCpds
CompsP[[i]]=FoundComps[[i]]
names(CompsP)[[i]]=paste("Compounds_",i,sep="")
if(is.null(LeadCpds)){
stop("In the Compounds element, specify an element LeadCpds")
}
group <- factor(ifelse(colnames(GeneExpr) %in% LeadCpds, 1, 0))
if(class(GeneExpr)[1]=="ExpressionSet"){
GeneExpr$LeadCmpds<-group
DElead <- limmaTwoLevels(GeneExpr,"LeadCmpds")
allDE <- a4Core::topTable(DElead, n = length(DElead@MArrayLM$genes$SYMBOL),sort.by="p")
if(is.null(allDE$ID)){
allDE$Genes <- rownames(allDE)
}
else
{
allDE$Genes=allDE$ID
}
if(is.null(topG)){
topG=length(which(allDE$adj.P.Val<=sign))
}
TopDE <- allDE[1:topG, ]
Genes <- list(TopDE,allDE)
names(Genes)<-c("TopDE","AllDE")
}
else{
label.factor = factor(group)
design = model.matrix(~label.factor)
fit = lmFit(GeneExpr,design=design)
fit = eBayes(fit)
allDE = limma::topTable(fit,coef=2,adjust="fdr",n=dim(GeneExpr)[1], sort.by="p")
if(is.null(allDE$ID)){
allDE$ID <- rownames(allDE)
}
if(is.null(topG)){
topG=length(which(allDE$adj.P.Val<=sign))
}
TopDE<-allDE[1:topG,]
Genes <- list(TopDE,allDE)
names(Genes)<-c("TopDE","AllDE")
}
FoundGenes[[i]]=Genes
TopDEP[[i]]=FoundGenes[[i]]
names(TopDEP)[i]=paste("genes_",i,sep="")
names(FoundGenes)=paste("Genes_",i,sep="")
pvalsgenes[[i]]=Genes$AllDE$P.Value
names(pvalsgenes[[i]])=Genes$AllDE$ID
names(pvalsgenes)[i]=paste("pvals_",i,sep="")
}
}
else{
pvalsgenes=list()
TopDEP=list()
for(i in 1:length(FoundGenes)){
#names(FoundGenes)[i]=paste("Genes_",i,sep="")
TopDEP[[i]]=FoundGenes[[i]]
names(TopDEP)[i]=paste("genes_",i,sep="")
pvalsgenes[[i]]=FoundGenes[[i]]$AllDE$P.Value
names(pvalsgenes[[i]])=FoundGenes[[i]]$AllDE$ID
names(pvalsgenes)[i]=paste("pvals_",i,sep="")
}
FoundComps=FindElement("Compounds",Object)
CompsP=list()
for(i in 1:length(FoundComps)){
if(is.null(FoundComps[[i]]$LeadCpds)){
CompsP[[i]]="No LeadCpds specified"
}
else{
CompsP[[i]]=FoundComps[[i]]
names(CompsP)[[i]]=paste("Compounds_",i,sep="")
}
}
}
return(list(pvalsgenes=pvalsgenes,Compounds=CompsP,Genes=TopDEP))
}
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