## ------------------------------------------------------------------------ library(TSCAN) data(lpsdata) procdata <- preprocess(lpsdata) ## ------------------------------------------------------------------------ lpsmclust <- exprmclust(procdata) ## ------------------------------------------------------------------------ plotmclust(lpsmclust) ## ------------------------------------------------------------------------ lpsorder <- TSCANorder(lpsmclust) lpsorder ## ------------------------------------------------------------------------ diffval <- difftest(procdata,lpsorder) #Selected differentially expressed genes under qvlue cutoff of 0.05 head(row.names(diffval)[diffval$qval < 0.05]) ## ------------------------------------------------------------------------ STAT2expr <- log2(lpsdata["STAT2",]+1) singlegeneplot(STAT2expr, TSCANorder(lpsmclust,flip=TRUE,orderonly=FALSE)) ## ------------------------------------------------------------------------ subpopulation <- data.frame(cell = colnames(procdata), sub = ifelse(grepl("Unstimulated",colnames(procdata)),0,1), stringsAsFactors = FALSE) #Comparing ordering with or without marker gene information order1 <- TSCANorder(lpsmclust) order2 <- TSCANorder(lpsmclust, c(1,2,3)) orders <- list(order1,order2) ## ------------------------------------------------------------------------ orderscore(subpopulation, orders)