## ----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()