library('mGSZ2');
runMGSZ2 <- function(exprMatrix, classes, ownGsets, input, session) {
selGsets <- input$gsetsSelection;
progress <- Progress$new(session);
progress$set(message='Loading gene sets.', detail='');
inSymbol <- input$geneSymbol;
gsets <- loadGsets(selGsets, ownGsets, inSymbol); # load selected gene sets
actCtrst <- input$selectedCtrst;
actCtrst <- strsplit(actCtrst, ' -vs- ')[[1]];
exprMatrix <- exprMatrix[, classes %in% actCtrst];
classes <- classes[classes %in% actCtrst];
progress$set(message='Starting mGSZ2 analysis.', detail='');
rankFn <- 'MA';
if (input$rnaSeqData)
rankFn <- 'RNA';
mGszRes <- mGSZ2(exprMatrix, gsets, classes, rankFn);
# genesRank <- rankFn(exprMatrix, classes);
progress$close();
updateTabsetPanel(session, inputId='maintab', selected='mGsz2Restab');
return(mGszRes);
}
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