## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(warning = FALSE, message = FALSE) ## ---- eval=F, echo=T---------------------------------------------------------- # ## install ZetaSuite R package # install.packages("ZetaSuite") # # ## load ZetaSuite R pakcage # library(ZetaSuite) ## ----workflow1, message=FALSE, include=FALSE---------------------------------- library(ZetaSuite) data(countMat) data(negGene) data(posGene) qcList <- QC(countMat,negGene,posGene) ## ----workflow1.1, eval=F, echo=T---------------------------------------------- # library(ZetaSuite) # data(countMat) # data(negGene) # data(posGene) # qcList <- QC(countMat,negGene,posGene) ## ---- fig.height = 4, fig.width = 6, fig.align = "center"--------------------- qcList[[2]] ## ---- fig.height = 3, fig.width = 8, fig.align = "center"--------------------- qcList[[1]] ## ---- fig.height = 4, fig.width = 8, fig.align = "center"--------------------- grid::grid.draw(qcList[[3]]) ## ---- fig.height = 4, fig.width = 6, fig.align = "center"--------------------- qcList[[4]] ## ----workflow2---------------------------------------------------------------- data(countMat) data(negGene) ZscoreVal <- Zscore(countMat,negGene) ZscoreVal[1:5,1:5] ## ----workflow3, fig.height = 4, fig.width = 4, fig.align = "center"----------- data(countMat) data(negGene) data(posGene) ZscoreVal <- Zscore(countMat,negGene) ECList <- EventCoverage(ZscoreVal,negGene,posGene,binNum=100,combine=TRUE) ECList[[2]][[1]] ECList[[2]][[2]] ## ----workflow4---------------------------------------------------------------- data(ZseqList) data(SVMcurve) data(countMat) data(negGene) ZscoreVal <- Zscore(countMat,negGene) zetaData <- Zeta(ZscoreVal,ZseqList,SVM=FALSE) ## ----workflow5, fig.height = 3, fig.width = 6, fig.align = "center"----------- data(nonExpGene) data(negGene) data(posGene) data(ZseqList) data(countMat) ZscoreVal <- Zscore(countMat,negGene) zetaData <- Zeta(ZscoreVal,ZseqList,SVM=FALSE) cutoffval <- FDRcutoff(zetaData,negGene,posGene,nonExpGene,combine=TRUE) cutoffval[[2]][[1]] cutoffval[[2]][[2]] ## ----sessionInfo-------------------------------------------------------------- sessionInfo()