## ----foo,cache=FALSE,include=FALSE,echo=FALSE---- library(qvalue) options(keep. txt)。source = TRUE, width = 48) foo <- packageDescription("qvalue") ## ----引用qvalue，eval = FALSE ----------------- # 引用(“qvalue ") ## ---- help_qvalue ------------------------------ 帮助(包= " qvalue ") ## ---- quick_p ---------------------------------- 库(qvalue)数据(hedenfalk) pvalues < - $ p hedenfalk qobj < - qvalue (p = pvalues) # #——quick_stat ------------------------------- 库(qvalue)数据(hedenfalk) obs_stats < - hedenfalk stat null_stats < - hedenfalk stat0美元pvalues < empPvals(统计= obs_stats,stat0 = null_stats) qobj < - qvalue (p = pvalues) # #——quick_access ----------------------------- qvalues < - qobj qvalues₀< - qobj₀lfdr <美元——qobj lfdr # #美元——quick_sumviz eval = FALSE ----------------- # 总结(qobj) #嘘(qobj) #地块(qobj) # #——load_qvalue ------------------------------ 数据(hedenfalk)名称(hedenfalk) # #——obsnullstat,取决于美元=“load_qvalue”——null_stats < - hedenfalk stat0 obs_stats < - hedenfalk stat pvalues < - empPvals美元(统计= obs_stats stat0 = null_stats,pool =FALSE) ## ----pvalue_hist2, dependson=c("load_qvalue"， "quick_p")， ---- 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="有问题的p值"，xlab="蓄意错误，模拟的p值")## ----run_qvalue，取决于= " load_qvalue”——qobj < - qvalue (p = hedenfalk $ p) # #——outNames,取决于= " run_qvalue "--------- 名(qobj) # #——summary_qvalue,取决于=“run_qvalue”——总结(qobj) # #,₀取决于= " run_qvalue "-------------- ₀< - qobj₀# #美元,₀取决于= " load_qvalue "---------- ₀< -₀(p = hedenfalk $ p,λ= seq(0.1, 0.9, 0.1),₀。method ="平滑")names(pi0) ## ----qvalue_ext, dependson="run_qvalue"，图.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. value, fdr. value, fdr. value ="run_qvalue"， fdr。水平= 0.1)# qobj美元重要# #——lfdr,取决于= " run_qvalue "------------- localFDR < - qobj lfdr # #美元——lfdr_f,取决于= " load_qvalue "---------- localFDR < - lfdr (p = hedenfalk $ p) # #——plot_qobj,取决于= c(“load_qvalue”、“run_qvalue”),fig.width =“\ textwidth”——情节(qobj) # #——hist_qobj,取决于= c(“load_qvalue”、“run_qvalue”),fig.width =“\ textwidth”——嘘(qobj)