Nothing
PredActScore <- function(prNet.o,data.m){
if(length(which(is.na(data.m))) > 0){
print("missing data in data.m must be imputed before proceeding");
}
### next standardize rows of data matrix
StdRow <- function(tmp.v){
out.v <- (tmp.v-mean(tmp.v))/sqrt(var(tmp.v));
return(out.v);
}
stdata.m <- data.m;
for(r in 1:nrow(data.m)){
stdata.m[r,] <- StdRow(data.m[r,]);
}
match(rownames(prNet.o$pradjMC),rownames(stdata.m)) -> idx;
which(is.na(idx)) -> idx.na
naF <- round(length(idx.na)/length(idx),2)
print(paste("Found ",100-100*naF,"% of maximally connected pruned network genes in the data",sep=""));
if (naF==1){
print("no gene overlap between new data set and pruned network, can't perform prediction")
}
else {
setdiff(1:length(idx),idx.na) -> idx.sel;
tmp.m <- stdata.m[idx[idx.sel],];
tmpA.m <- prNet.o$pradjMC[idx.sel,idx.sel];
k.v <- apply(tmpA.m,1,sum);
genescores.m <- k.v*sign(prNet.o$signMC[idx.sel])*tmp.m;
score.v <- apply(genescores.m,2,sum)/sqrt(sum(k.v*k.v));
}
return(list(adj=tmpA.m,sign=prNet.o$signMC[idx.sel],score=score.v,degree=k.v));
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.