## ----------------------------------------------------------------------------- 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)