## ----style, eval=TRUE, echo=FALSE, results='asis'-------------------------- BiocStyle::latex(use.unsrturl=FALSE) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # library(PROPER) # sim.opts.Cheung = RNAseq.SimOptions.2grp(ngenes = 20000, p.DE=0.05, # lOD="cheung", lBaselineExpr="cheung") ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # sim.opts.Bottomly = RNAseq.SimOptions.2grp(ngenes = 20000, p.DE=0.05, # lOD="bottomly", lBaselineExpr="bottomly") ## ----echo=TRUE,eval=FALSE,result=FALSE------------------------------------- # simres = runSims(Nreps = c(3, 5, 7, 10), sim.opts=sim.opts.Cheung, # DEmethod="edgeR", nsims=20) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # powers = comparePower(simres, alpha.type="fdr", alpha.nominal=0.1, # stratify.by="expr", delta=0.5) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # summaryPower(powers) ## ----eval=FALSE,echo=TRUE-------------------------------------------------- # plotPower(powers) ## ----eval=FALSE,echo=TRUE-------------------------------------------------- # plotPowerTD(powers) ## ----eval=FALSE,echo=TRUE-------------------------------------------------- # plotFDcost(powers) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # plotAll(powers) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # power.seqDepth(simres, powers) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # powers = comparePower(simres, alpha.type="fdr", alpha.nominal=0.1, # strata = c(0, 10, 2^(1:7)*10, Inf), filter.by="expr", # strata.filtered=1, stratify.by="expr", delta=0.5) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # powers = comparePower(simres, alpha.type="fdr", alpha.nominal=0.1, # stratify.by="dispersion", target.by="effectsize", delta=1) ## ----echo=TRUE,eval=FALSE-------------------------------------------------- # powers = comparePower(simres, alpha.type="pval", alpha.nominal=0.001, # stratify.by="dispersion", target.by="effectsize", delta=1) ## ----echo=TRUE, result=TRUE------------------------------------------------ sessionInfo()