## ----ultaQuick----------------------------------------------------------- library("RIVER") ## ------------------------------------------------------------------------ filename <- system.file("extdata", "simulation_RIVER.gz", package="RIVER") dataInput <- getData(filename) # import experimental data ## ------------------------------------------------------------------------ print(dataInput) Feat <- t(Biobase::exprs(dataInput)) # genomic features (G) Out <- as.numeric(unlist(dataInput$Outlier))-1 # outlier status (E) ## ------------------------------------------------------------------------ head(Feat) head(Out) ## ------------------------------------------------------------------------ evaROC <- evaRIVER(dataInput) ## ------------------------------------------------------------------------ cat('AUC (GAM-genomic annotation model) = ', round(evaROC$GAM_auc,3), '\n') cat('AUC (RIVER) = ', round(evaROC$RIVER_auc,3), '\n') cat('P-value ', format.pval(evaROC$pvalue, digits=2, eps=0.001), '***\n') ## ------------------------------------------------------------------------ par(mar=c(6.1, 6.1, 4.1, 4.1)) plot(NULL, xlim=c(0,1), ylim=c(0,1), xlab="False positive rate", ylab="True positive rate", cex.axis=1.3, cex.lab=1.6) abline(0, 1, col="gray") lines(1-evaROC$RIVER_spec, evaROC$RIVER_sens, type="s", col='dodgerblue', lwd=2) lines(1-evaROC$GAM_spec, evaROC$GAM_sens, type="s", col='mediumpurple', lwd=2) legend(0.7,0.2,c("RIVER","GAM"), lty=c(1,1), lwd=c(2,2), col=c("dodgerblue","mediumpurple"), cex=1.2, pt.cex=1.2, bty="n") title(main=paste("AUC: RIVER = ", round(evaROC$RIVER_auc,3), ", GAM = ", round(evaROC$GAM_auc,3), ", P = ", format.pval(evaROC$pvalue, digits=2, eps=0.001),sep="")) ## ------------------------------------------------------------------------ postprobs <- appRIVER(dataInput) ## ------------------------------------------------------------------------ example_probs <- data.frame(Subject=postprobs$indiv_name, Gene=postprobs$gene_name, RIVERpp=postprobs$RIVER_posterior, GAMpp=postprobs$GAM_posterior) head(example_probs) ## ------------------------------------------------------------------------ plotPosteriors(postprobs, outliers=as.numeric(unlist(dataInput$Outlier))-1) ## ------------------------------------------------------------------------ filename <- system.file("extdata", "simulation_RIVER.gz", package="RIVER") dataInput <- getData(filename) # import experimental data evaROC <- evaRIVER(dataInput, pseudoc=50, theta_init=matrix(c(.99, .01, .3, .7), nrow=2), costs=c(100, 10, 1, .1, .01, 1e-3, 1e-4), verbose=TRUE) ## ------------------------------------------------------------------------ postprobs <- appRIVER(dataInput, pseudoc=50, theta_init=matrix(c(.99, .01, .3, .7), nrow=2), costs=c(100, 10, 1, .1, .01, 1e-3, 1e-4), verbose=TRUE) ## ------------------------------------------------------------------------ print(postprobs$fitRIVER$beta) ## ------------------------------------------------------------------------ print(postprobs$fitRIVER$theta) ## ------------------------------------------------------------------------ filename <- system.file("extdata", "simulation_RIVER.gz", package = "RIVER") system(paste('zcat ', filename, " | head -2", sep=""), ignore.stderr=TRUE) ## ------------------------------------------------------------------------ YourInputToRIVER <- getData(filename) # import experimental data ## ---- eval=FALSE--------------------------------------------------------- # ## try http:// if https:// URLs are not supported # source("https://bioconductor.org/biocLite.R") # biocLite("RIVER") ## --------------------------------------------------------------------------------------------------------------------- ## Session info library('devtools') options(width=120) session_info()