CalcTPSig <- function(EdgeInfo,pathway="Pathway",EdgeFrom="GeneSymbol_a",EdgeTo="GeneSymbol_b",interaction="Interaction",ncomp=NULL,data,neigen=NULL) {
PathwayList <- unique(EdgeInfo[,pathway])
ScoreTab <- matrix(NA,ncol=ncol(data),nrow=length(PathwayList))
rownames(ScoreTab) <- PathwayList
for (path in PathwayList) {
Edge <- EdgeInfo[EdgeInfo$Pathway==path,]
AdjMat <- CalcAdj(EdgeFrom=Edge[,EdgeFrom],EdgeTo=Edge[,EdgeTo],interaction=Edge[,interaction])
if (is.null(AdjMat)) {
print(paste0("Adjacency matrix for ",path," is not available!"))
} else {
Score <- CalcScore(AdjMat=AdjMat,ncomp=ncomp,data=t(data),neigen=neigen)
if (length(Score)!=0) {
nonull <- sapply(Score,function(x) {!is.null(x)})
if (sum(nonull)>0) {
Score <- Score[nonull]
Score_summary <- rowSums(matrix(sapply(Score,function(x) as.numeric(x$Score)),ncol=length(Score)))
ScoreTab[path,] <- Score_summary
}
}
}
}
ScoreTab <- data.frame(ScoreTab,stringsAsFactors=FALSE)
colnames(ScoreTab) <- colnames(data)
return(ScoreTab)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.