### R code from vignette source 'vignettes/GeneSelectMMD/inst/doc/gsMMD.Rnw' ################################################### ### code chunk number 1: gsMMD.Rnw:494-510 ################################################### library(GeneSelectMMD) library(ALL) data(ALL) eSet1 <- ALL[1:100, ALL$BT == "B3" | ALL$BT == "T2"] mem.str <- as.character(eSet1$BT) nSubjects <- length(mem.str) memSubjects <- rep(0,nSubjects) # B3 coded as 0, T2 coded as 1 memSubjects[mem.str == "T2"] <- 1 obj.gsMMD <- gsMMD(eSet1, memSubjects, transformFlag = TRUE, transformMethod = "boxcox", scaleFlag = TRUE, quiet = TRUE) para <- obj.gsMMD$para print(round(para, 3)) ################################################### ### code chunk number 2: gsMMD.Rnw:513-531 (eval = FALSE) ################################################### ## library(GeneSelectMMD) ## library(ALL) ## data(ALL) ## eSet1 <- ALL[1:100, ALL$BT == "B3" | ALL$BT == "T2"] ## mat <- exprs(eSet1) ## ## mem.str <- as.character(eSet1$BT) ## nSubjects <- length(mem.str) ## memSubjects <- rep(0,nSubjects) ## # B3 coded as 0, T2 coded as 1 ## memSubjects[mem.str == "T2"] <- 1 ## ## obj.gsMMD <- gsMMD.default(mat, memSubjects, iniGeneMethod = "Ttest", ## transformFlag = TRUE, transformMethod = "boxcox", scaleFlag = TRUE, ## quiet=TRUE) ## para <- obj.gsMMD$para ## print(round(para, 3)) ## ################################################### ### code chunk number 3: gsMMD.Rnw:537-576 (eval = FALSE) ################################################### ## library(GeneSelectMMD) ## library(ALL) ## data(ALL) ## eSet1 <- ALL[1:100, ALL$BT == "B3" | ALL$BT == "T2"] ## ## mem.str <- as.character(eSet1$BT) ## nSubjects <- length(mem.str) ## memSubjects <- rep(0,nSubjects) ## # B3 coded as 0, T2 coded as 1 ## memSubjects[mem.str == "T2"] <- 1 ## ## myWilcox <- ## function(x, memSubjects, alpha = 0.05) ## { ## xc <- x[memSubjects == 1] ## xn <- x[memSubjects == 0] ## ## m <- sum(memSubjects == 1) ## res <- wilcox.test(x = xc, y = xn, conf.level = 1 - alpha) ## res2 <- c(res$p.value, res$statistic - m * (m + 1) / 2) ## names(res2) <- c("p.value", "statistic") ## ## return(res2) ## } ## ## mat <- exprs(eSet1) ## tmp <- t(apply(mat, 1, myWilcox, memSubjects = memSubjects)) ## colnames(tmp) <- c("p.value", "statistic") ## memIni <- rep(2, nrow(mat)) ## memIni[tmp[, 1] < 0.05 & tmp[, 2] > 0] <- 1 ## memIni[tmp[, 1] < 0.05 & tmp[, 2] < 0] <- 3 ## ## print(table(memIni)) ## ## obj.gsMMD <- gsMMD2(eSet1, memSubjects, memIni, transformFlag = TRUE, ## transformMethod = "boxcox", scaleFlag = TRUE, quiet = TRUE) ## para <- obj.gsMMD$para ## print(round(para, 3)) ## ################################################### ### code chunk number 4: gsMMD.Rnw:579-620 (eval = FALSE) ################################################### ## library(GeneSelectMMD) ## library(ALL) ## data(ALL) ## eSet1 <- ALL[1:100, ALL$BT == "B3" | ALL$BT == "T2"] ## mat <- exprs(eSet1) ## ## mem.str <- as.character(eSet1$BT) ## nSubjects <- length(mem.str) ## memSubjects <- rep(0,nSubjects) ## # B3 coded as 0, T2 coded as 1 ## memSubjects[mem.str == "T2"] <- 1 ## ## myWilcox <- ## function(x, memSubjects, alpha = 0.05) ## { ## xc <- x[memSubjects == 1] ## xn <- x[memSubjects == 0] ## ## m <- sum(memSubjects == 1) ## res <- wilcox.test(x = xc, y = xn, conf.level = 1 - alpha) ## res2 <- c(res$p.value, res$statistic - m * (m + 1) / 2) ## names(res2) <- c("p.value", "statistic") ## ## return(res2) ## } ## ## tmp <- t(apply(mat, 1, myWilcox, memSubjects = memSubjects)) ## colnames(tmp) <- c("p.value", "statistic") ## memIni <- rep(2, nrow(mat)) ## memIni[tmp[, 1] < 0.05 & tmp[, 2] > 0] <- 1 ## memIni[tmp[, 1] < 0.05 & tmp[, 2] < 0] <- 3 ## ## print(table(memIni)) ## ## obj.gsMMD <- gsMMD2.default(mat, memSubjects, memIni = memIni, ## transformFlag = TRUE, transformMethod = "boxcox", scaleFlag = TRUE, ## quiet=TRUE) ## para <- obj.gsMMD$para ## print(round(para, 3)) ## ## ################################################### ### code chunk number 5: gsMMD.Rnw:659-661 ################################################### print(round(errRates(obj.gsMMD), 3)) ################################################### ### code chunk number 6: gsMMD.Rnw:677-686 ################################################### plotHistDensity(obj.gsMMD, plotFlag = "case", mytitle = "Histogram of gene expression levels for T2\nimposed with estimated density (case)", plotComponent = TRUE, x.legend = c(0.8, 3), y.legend = c(0.3, 0.4), numPoints = 500, cex.main = 1, cex = 1)