## ----setup, include = FALSE---------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----showDataExample, message=FALSE, warning=FALSE----------------------- library(PowerExplorer) data("exampleProteomicsData") head(exampleProteomicsData$dataMatrix) ## ------------------------------------------------------------------------ show(exampleProteomicsData$groupVec) ## ------------------------------------------------------------------------ colnames(exampleProteomicsData$dataMatrix) ## ----est run, echo=TRUE, fig.keep='none', message=FALSE, warning=FALSE---- library(PowerExplorer) data("exampleProteomicsData") res <- estimatePower(inputObject = exampleProteomicsData$dataMatrix, groupVec = exampleProteomicsData$groupVec, isLogTransformed = FALSE, dataType = "Proteomics", minLFC = 0.5, enableROTS = TRUE, paraROTS = list(B = 1000, K = NULL), alpha = 0.05, ST = 50, seed = 345, showProcess = FALSE, saveResultData = FALSE ) ## ----plot estimated power------------------------------------------------ plotEstPwr(res) ## ------------------------------------------------------------------------ res ## ------------------------------------------------------------------------ data(exampleObject) listEstPwr(exampleObject, decreasing = TRUE, top = 10) ## ------------------------------------------------------------------------ listEstPwr(exampleObject, selected = c("ENSMUSG00000000303", "ENSMUSG00000087272", "ENSMUSG00000089921")) ## ----prediction run2, message=FALSE, warning=FALSE----------------------- data("exampleProteomicsData") res <- predictPower(inputObject = res, groupVec = exampleProteomicsData$groupVec, isLogTransformed = FALSE, dataType = "Proteomics", minLFC = 0.5, rangeSimNumRep = c(5, 10, 15, 20), enableROTS = TRUE, paraROTS = list(B = 1000, K = NULL), alpha = 0.05, ST = 50, seed = 345) ## ----LinePlot------------------------------------------------------------ plotPredPwr(res, LFCscale = 0.5) ## ------------------------------------------------------------------------ res ## ------------------------------------------------------------------------ listPredPwr(exampleObject, decreasing = TRUE, top = 10) ## ------------------------------------------------------------------------ listPredPwr(exampleObject, selected = c("ENSMUSG00000000303", "ENSMUSG00000087272", "ENSMUSG00000089921"))