Nothing
SIMoNeNet.default <-
function (x,DEGeneExpr,GenesAnnotations=NULL, ...)
{
SIMoNeThetas<-x$Theta
SIMoNeThetas[lower.tri(SIMoNeThetas,diag=T)]<-0
Genes1=rownames(SIMoNeThetas)[which(SIMoNeThetas!=0,arr.ind=T)[,"row"]]
Genes2=colnames(SIMoNeThetas)[which(SIMoNeThetas!=0,arr.ind=T)[,"col"]]
Graph<-as.data.frame(matrix(NA,ncol=6,nrow=length(Genes1)))
names(Graph)<-c("node1","node2","Interaction","Theta","Rho","P.Value")
for (i in 1:nrow(Graph))
{
Gene1<-Genes1[i]
Gene2<-Genes2[i]
TestSpearman=pspearman::spearman.test(DEGeneExpr$DataExpression[,Gene2],DEGeneExpr$DataExpression[,Gene1],approximation="AS89")
Graph[i,]<-c(Gene1,Gene2,"SIMoNeInference",SIMoNeThetas[Gene1,Gene2],TestSpearman$estimate,TestSpearman$p.value)
}
Graph$Theta<-as.numeric(Graph$Theta)
Graph$Rho<-as.numeric(Graph$Rho)
Graph$P.Value<-as.numeric(Graph$P.Value)
Genes<-unique(c(Genes1,Genes2))
DEGenes<-DEGeneExpr$DEGenesResults[rownames(DEGeneExpr$DEGenesResults) %in% Genes,]
SIMoNeNet<-list(Edges=Graph,DEGenes=DEGenes,clusters=x$clusters,name=x$name)
if(!is.null(GenesAnnotations))
{
Annotations<-GenesAnnotations[rownames(GenesAnnotations) %in% Genes,]
SIMoNeNet$Annotations<-Annotations
}
class(SIMoNeNet)<-"SIMoNeNet"
SIMoNeNet
}
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