Nothing
getNormalizedData=function(model,data,controls=NULL){
dd=data
if (!is.null(controls)) {
dd=dd[!(dd$gene %in% controls),]
}
prr=predict(model,type="terms",marginal=~sample)
dd$pred=prr[1:nrow(dd)]
predicted=c()
for (g in unique(dd$gene)) {
if (g %in% controls) { next }
gs=c();coo=c()
for(s in unique(dd$sample)) {
gs=append(gs,dd$pred[dd$gene==g & dd$sample==s][1]/log(2))
coo=rbind(coo,dd[dd$gene==g & dd$sample==s,][1,4:(ncol(dd)-1)])
}
predicted=cbind(predicted,gs)
}
predicted=data.frame(predicted)
conditions=data.frame(coo)
names(predicted)=unique(dd$gene)
row.names(predicted)= unique(dd$sample)
row.names(conditions)= unique(dd$sample)
return(list("normData"=predicted,"conditions"=conditions))
}
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