## ----foo,cache=FALSE,include=FALSE,echo=FALSE---- library(qvalue) options(keep.source = TRUE, width = 48) foo <- packageDescription("qvalue") ## ----citingqvalue, eval=FALSE----------------- # citation("qvalue") ## ----help_qvalue------------------------------ help(package="qvalue") ## ----quick_p---------------------------------- library(qvalue) data(hedenfalk) pvalues <- hedenfalk$p qobj <- qvalue(p = pvalues) ## ----quick_stat------------------------------- library(qvalue) data(hedenfalk) obs_stats <- hedenfalk$stat null_stats <- hedenfalk$stat0 pvalues <- empPvals(stat = obs_stats, stat0 = null_stats) qobj <- qvalue(p = pvalues) ## ----quick_access----------------------------- qvalues <- qobj$qvalues pi0 <- qobj$pi0 lfdr <- qobj$lfdr ## ----quick_sumviz, eval=FALSE----------------- # summary(qobj) # hist(qobj) # plot(qobj) ## ----load_qvalue------------------------------ data(hedenfalk) names(hedenfalk) ## ----obsnullstat, dependson="load_qvalue"----- null_stats <- hedenfalk$stat0 obs_stats <- hedenfalk$stat pvalues <- empPvals(stat = obs_stats, stat0 = null_stats, pool = FALSE) ## ----pvalue_hist2, dependson=c("load_qvalue", "quick_p"), fig.height=3, fig.width=5---- hist(hedenfalk$p, nclass = 20) ## ----pvalue_histBad, dependson=c("load_qvalue", "quick_p"), echo=FALSE, fig.height=3, fig.width=5---- set.seed(478) p2 = c(hedenfalk$p, (runif(450, min=0.7, max=1))^(0.33)) somethingsWrong = list(p=p2) hist(somethingsWrong$p, nclass=20, main="Problematic p-values", xlab="intentionally bad, simulated p-values") ## ----run_qvalue, dependson="load_qvalue"------ qobj <- qvalue(p = hedenfalk$p) ## ----outNames, dependson="run_qvalue"--------- names(qobj) ## ----summary_qvalue, dependson="run_qvalue"---- summary(qobj) ## ----pi0, dependson="run_qvalue"-------------- pi0 <- qobj$pi0 ## ----pi0est, dependson="load_qvalue"---------- pi0 <- pi0est(p = hedenfalk$p, lambda = seq(0.1, 0.9, 0.1), pi0.method = "smoother" ) names(pi0) ## ----qvalue_ext, dependson="run_qvalue", fig.height=4---- qvalues <- qobj$qvalues ## ----tmp, dependson=c("qvalue_ext", "run_qvalue")---- max(qvalues[qobj$pvalues <= 0.01]) ## ----fdrlevel, dependson="run_qvalue", eval=FALSE---- # qobj_fdrlevel <- qvalue(p = hedenfalk$p, fdr.level = 0.1) # qobj$significant ## ----lfdr, dependson="run_qvalue"------------- localFDR <- qobj$lfdr ## ----lfdr_f, dependson="load_qvalue"---------- localFDR <- lfdr(p = hedenfalk$p) ## ----plot_qobj, dependson=c("load_qvalue", "run_qvalue"), fig.width='\textwidth'---- plot(qobj) ## ----hist_qobj, dependson=c("load_qvalue", "run_qvalue"), fig.width='\textwidth'---- hist(qobj)