## ---- message=FALSE------------------------------------------------------ library(saps) ## ------------------------------------------------------------------------ followup <- rep(1, 25) ## ------------------------------------------------------------------------ time <- c(25, 27, 24, 21, 26, sample(1:3, 20, TRUE))*365 ## ------------------------------------------------------------------------ dat <- matrix(rnorm(25*100), nrow=25, ncol=100) colnames(dat) <- as.character(1:100) ## ------------------------------------------------------------------------ set1 <- sample(colnames(dat), 5) set2 <- sample(colnames(dat), 5) ## ------------------------------------------------------------------------ genesets <- rbind(set1, set2) ## ----firstrun, message=FALSE--------------------------------------------- results <- saps(genesets, dat, time, followup, random.samples=100) ## ------------------------------------------------------------------------ saps_table <- results$saps_table saps_table[1:7] ## ------------------------------------------------------------------------ dat2 <- dat dat2[1:5, set1] <- dat2[1:5, set1]+10 ## ----secondrun, message=FALSE-------------------------------------------- results <- saps(genesets, dat2, time, followup, random.samples=100) saps_table <- results$saps_table saps_table[1:7] ## ------------------------------------------------------------------------ saps_table[8:11] ## ---- message=FALSE------------------------------------------------------ set1 <- results$genesets[["set1"]] plotKM(set1, time/365, followup, x.label="Overall survival (years)") ## ------------------------------------------------------------------------ plotRandomDensity(set1) ## ------------------------------------------------------------------------ plotEnrichment(set1, results$rankedGenes) ## ----qvalue, message=FALSE----------------------------------------------- results <- saps(genesets, dat2, time, followup, random.samples=100, compute_qvalue=TRUE, qvalue.samples=10) saps_table <- results$saps_table saps_table[, c("saps_qvalue", "saps_qvalue_adj")] ## ------------------------------------------------------------------------ set1 <- results$genesets[["set1"]] plotSapsScoreDensity(set1)