## ----para, echo = FALSE, results='hide'--------------------------------------- BiocStyle::markdown() knitr::opts_chunk$set(dev="png",fig.show="hold", fig.width=4,fig.height=4.5,fig.align="center", message=FALSE,collapse=TRUE) ## ----library------------------------------------------------------------------ library(rnaseqcomp) ## ----data--------------------------------------------------------------------- # load the dataset in this package data(simdata) class(simdata) names(simdata) ## ----meta--------------------------------------------------------------------- condInfo <- factor(simdata$samp$condition) repInfo <- factor(simdata$samp$replicate) evaluationFeature <- rep(TRUE, nrow(simdata$meta)) calibrationFeature <- simdata$meta$house & simdata$meta$chr == 'chr1' unitReference <- 1 ## ----filter------------------------------------------------------------------- dat <- signalCalibrate(simdata$quant, condInfo, repInfo, evaluationFeature, calibrationFeature, unitReference, calibrationFeature2 = calibrationFeature) class(dat) show(dat) ## ----sd----------------------------------------------------------------------- plotSD(dat,ylim=c(0,1.4)) ## ----nonexpplot--------------------------------------------------------------- plotNE(dat,xlim=c(0.5,1)) ## ----tx2---------------------------------------------------------------------- plot2TX(dat,genes=simdata$meta$gene,ylim=c(0,0.6)) ## ----diffroc------------------------------------------------------------------ plotROC(dat,simdata$meta$positive,simdata$meta$fcsign,ylim=c(0,0.8)) ## ----difffc------------------------------------------------------------------- simdata$meta$fcsign[simdata$meta$fcstatus == "off.on"] <- NA plotFC(dat,simdata$meta$positive,simdata$meta$fcsign,ylim=c(0,1.2))