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# This function chooses a single plobe per gene based on a kME table
collapseRowsUsingKME <- function (MM, Gin, Pin=NULL, kMEcols = 1:dim(MM)[2]){
if (is.null(Pin)) Pin = rownames(MM)
rownames(MM) = Pin
Gout = as.character(sort(unique(Gin)))
cors = MM[,kMEcols]
maxC = apply(cors,1,max)
MMout = matrix(0, nrow = length(Gout), ncol = dim(MM)[2])
colnames(MMout) = colnames(MM)
rownames(MMout) = Gout
MM = as.matrix(MM)
keepThese = NULL
for (g in 1:length(Gout)){
maxCg = maxC
maxCg[Gin!=Gout[g]] = -1000
keep = which(maxCg==max(maxCg))[1]
MMout[g,] = MM[keep,]
keepThese = c(keepThese, keep)
}
group2Row = cbind(Gout,Pin[keepThese])
colnames(group2Row) = c("group","selectedRowID")
selectedRow = is.element(1:length(Pin),keepThese)
out = list(MMout, group2Row, selectedRow)
names(out) = c("MMcollapsed","group2Row", "selectedRow")
return(out)
}
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