### R code from vignette source 'vignettes/dressCheck/inst/doc/short.Rnw' ################################################### ### code chunk number 1: do1 ################################################### psurv = function (x, digits = max(options()$digits - 4, 3), ...) { saveopt <- options(digits = digits) on.exit(options(saveopt)) if (!inherits(x, "survdiff")) stop("Object is not the result of survdiff") if (!is.null(cl <- x$call)) { } omit <- x$na.action if (length(omit)) { } if (length(x$n) == 1) { z <- sign(x$exp - x$obs) * sqrt(x$chisq) temp <- c(x$obs, x$exp, z, signif(1 - pchisq(x$chisq, 1), digits)) names(temp) <- c("Observed", "Expected", "Z", "p") print(temp) } else { if (is.matrix(x$obs)) { otmp <- apply(x$obs, 1, sum) etmp <- apply(x$exp, 1, sum) } else { otmp <- x$obs etmp <- x$exp } df <- (sum(1 * (etmp > 0))) - 1 temp <- cbind(x$n, otmp, etmp, ((otmp - etmp)^2)/etmp, ((otmp - etmp)^2)/diag(x$var)) dimnames(temp) <- list(names(x$n), c("N", "Observed", "Expected", "(O-E)^2/E", "(O-E)^2/V")) uu <- 1 - pchisq(x$chisq, df) } uu } library(dressCheck) library(chron) library(survival) data(DrAsGiven) data(corrp116) an = as.numeric pdf(file="twox3.pdf", width=8, height=5) par(mfrow=c(2,3)) plot(an(exprs(corrp116["213350_at",]))~chron(corrp116$rundate), main="(a)", xlab="array run date", ylab="RMA+SFR expression of RPS11") CC = cut(chron(corrp116$rundate),2) with(pData(corrp116), d0 <<- survdiff(Surv(Survival, dead)~CC, subset=CR==0)) with(pData(corrp116), plot(survfit(Surv(Survival, dead)~CC, subset=CR==0),col=c("red", "green"), lwd=3, xlab="Months", ylab="survival (%)", main="(b)")) text(37,.03, paste("logrank p=", round(psurv(d0),3))) #giv = DrAsGiven[intersect(featureNames(DrAsGiven), names(srcWts)),] #srcWtsL = srcWts[featureNames(giv)] #sco = t(exprs(giv))%*%srcWtsL #sdys = 1*(sco>median(sco)) #with(pData(DrAsGiven), plot(survfit(Surv(Survival, X0...alive...1...dead)~sdys, # subset=response.0.NR..1.CR==0),col=c("blue", "yellow"), lwd=3, # xlab="Months", ylab="survival (%)", main="(b)")) #with(pData(DrAsGiven), d1 <<- survdiff(Surv(Survival, X0...alive...1...dead)~sdys, # subset=response.0.NR..1.CR==0)) #text(37,.05, paste("logrank p=", round(psurv(d1),3))) data(srcWts) # get scoring coefficients, then restrict expression data to the # genes in the pathway signature corr = corrp116[intersect(featureNames(corrp116), names(srcWts)),] srcWtsL = srcWts[featureNames(corr)] # score the tumors sco = t(exprs(corr))%*%srcWtsL sdys = 1*(sco>median(sco)) # dichotomize with(pData(corrp116), plot(survfit(Surv(Survival, dead)~sdys, subset=CR==0),col=c("blue", "yellow"), lwd=3, xlab="Months", ylab="survival (%)", main="(c)")) with(pData(corrp116), d2 <<- survdiff(Surv(Survival, dead)~sdys, subset=CR==0)) text(37,.05, paste("logrank p=", round(psurv(d2),3))) data(e2f3Wts) corr = corrp116[intersect(featureNames(corrp116), names(e2f3Wts)),] eWtsL = e2f3Wts[featureNames(corr)] sco = t(exprs(corr))%*%eWtsL edys = 1*(sco