## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, crop = NA) ## ----warning = FALSE---------------------------------------------------------- suppressPackageStartupMessages({ library(countsimQC) library(DESeq2) }) data(countsimExample) countsimExample countsimExample <- lapply(countsimExample, function(cse) { cse[seq_len(1500), ] }) ## ----results = "hide", warning = FALSE, message = FALSE----------------------- tempDir <- tempdir() countsimQCReport(ddsList = countsimExample, outputFile = "countsim_report.html", outputDir = tempDir, outputFormat = "html_document", showCode = FALSE, forceOverwrite = TRUE, savePlots = TRUE, description = "This is my test report.", maxNForCorr = 25, maxNForDisp = Inf, calculateStatistics = TRUE, subsampleSize = 25, kfrac = 0.01, kmin = 5, permutationPvalues = FALSE, nPermutations = NULL) ## ----warning = FALSE---------------------------------------------------------- ggplots <- readRDS(file.path(tempDir, "countsim_report_ggplots.rds")) if (!dir.exists(file.path(tempDir, "figures"))) { dir.create(file.path(tempDir, "figures")) } generateIndividualPlots(ggplots, device = "pdf", nDatasets = 3, outputDir = file.path(tempDir, "figures")) ## ----------------------------------------------------------------------------- data(countsimExample_dfmat) names(countsimExample_dfmat) lapply(countsimExample_dfmat, class) ## ----results = "hide", warning = FALSE, eval = FALSE-------------------------- # tempDir <- tempdir() # countsimQCReport(ddsList = countsimExample_dfmat, # outputFile = "countsim_report_dfmat.html", # outputDir = tempDir, outputFormat = "html_document", # showCode = FALSE, forceOverwrite = TRUE, # savePlots = TRUE, description = "This is my test report.", # maxNForCorr = 25, maxNForDisp = Inf, # calculateStatistics = TRUE, subsampleSize = 25, # kfrac = 0.01, kmin = 5, # permutationPvalues = FALSE, nPermutations = NULL) ## ----------------------------------------------------------------------------- sessionInfo()