Hi,

I was trying to fit the mogsa function on mutation matrix which is from miniACC dataset, MultiAssayExperiment package. However, it is able to create the supp data, but whenever I tried the mogsa function, it always gave me error that object r not found. I would be very thankful if somebody can give me some hints about how to fix it and what's the idea of creating supp data (eg. how to manually create supp data for your own gene dataset).

mutation <- assay(miniACC[[4]])

keggdb <- prepGraphite(db = pathways("hsapiens", "kegg")[1:50], id = "symbol")
keggdb <- lapply(keggdb, function(x) sub("SYMBOL:", "", x))

supp <- prepSupMoa(mutation, geneSets=keggdb, minMatch=1)

mgsa1 <- mogsa(x=mutation, sup=supp, nf=3, proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)

Error in new("mgsa", call = match.call(), moa = r, sup = supr) :
object 'r' not found