## ----'installDer', eval = FALSE--------------------------------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("regionReport") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----'citation'------------------------------------------------------------------------------------------------------- ## Citation info citation("regionReport") ## ----vignetteSetup, echo = FALSE, message = FALSE, warning = FALSE---------------------------------------------------- ## Track time spent on making the vignette startTimeVignette <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( derfinder = citation("derfinder")[1], regionReport = citation("regionReport")[1], knitrBootstrap = citation("knitrBootstrap"), BiocStyle = citation("BiocStyle"), ggbio = citation("ggbio"), ggplot2 = citation("ggplot2"), knitr = citation("knitr")[3], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], DT = citation("DT"), R = citation(), IRanges = citation("IRanges"), sessioninfo = citation("sessioninfo"), GenomeInfoDb = RefManageR::BibEntry( bibtype = "manual", key = "GenomeInfoDb", author = "Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès", title = "GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers", year = 2017, doi = "10.18129/B9.bioc.GenomeInfoDb" ), GenomicRanges = citation("GenomicRanges"), biovizBase = citation("biovizBase"), TxDb.Hsapiens.UCSC.hg19.knownGene = citation("TxDb.Hsapiens.UCSC.hg19.knownGene"), derfinderPlot = citation("derfinderPlot")[1], grid = citation("grid"), gridExtra = citation("gridExtra"), mgcv = citation("mgcv"), RColorBrewer = citation("RColorBrewer"), whikser = citation("whisker"), bumphunter = citation("bumphunter")[1], pheatmap = citation("pheatmap"), DESeq2 = citation("DESeq2"), edgeR1 = citation("edgeR")[1], edgeR2 = citation("edgeR")[2], edgeR6 = RefManageR::BibEntry("inbook", key = "edgeR6", author = "Chen, Yunshun and Lun, Aaron T. L. and Smyth, Gordon K.", title = "Differential expression analysis of complex RNA-seq experiments using edgeR", booktitle = "Statistical Analysis of Next Generation Sequencing Data", year = 2014, editor = "Datta, Somnath and Nettleton, Dan", publisher = "Springer", location = "New York", pages = "51-74" ), DEFormats = citation("DEFormats") ) ## ----overviewNotRun, eval = FALSE------------------------------------------------------------------------------------- # ## Load derfinder # library("derfinder") # regions <- genomeRegions$regions # # ## Assign chr length # library("GenomicRanges") # seqlengths(regions) <- c("chr21" = 48129895) # # ## The output will be saved in the 'derfinderReport-example' directory # dir.create("renderReport-example", showWarnings = FALSE, recursive = TRUE) # # ## Generate the HTML report # report <- renderReport(regions, "Example run", # pvalueVars = c( # "Q-values" = "qvalues", "P-values" = "pvalues" # ), densityVars = c( # "Area" = "area", "Mean coverage" = "meanCoverage" # ), # significantVar = regions$qvalues <= 0.05, nBestRegions = 20, # outdir = "renderReport-example" # ) ## ----loadDerfinder---------------------------------------------------------------------------------------------------- ## Load derfinder library("derfinder") ## The output will be saved in the "derfinderReport-example" directory dir.create("derfinderReport-example", showWarnings = FALSE, recursive = TRUE) ## ----runDerfinderFake, eval=FALSE------------------------------------------------------------------------------------- # ## Save the current path # initialPath <- getwd() # setwd(file.path(initialPath, "derfinderReport-example")) # # ## Generate output from derfinder # # ## Collapse the coverage information # collapsedFull <- collapseFullCoverage(list(genomeData$coverage), # verbose = TRUE # ) # # ## Calculate library size adjustments # sampleDepths <- sampleDepth(collapsedFull, # probs = c(0.5), nonzero = TRUE, # verbose = TRUE # ) # # ## Build the models # group <- genomeInfo$pop # adjustvars <- data.frame(genomeInfo$gender) # models <- makeModels(sampleDepths, testvars = group, adjustvars = adjustvars) # # ## Analyze chromosome 21 # analysis <- analyzeChr( # chr = "21", coverageInfo = genomeData, models = models, # cutoffFstat = 1, cutoffType = "manual", seeds = 20140330, groupInfo = group, # mc.cores = 1, writeOutput = TRUE, returnOutput = TRUE # ) # # ## Save the stats options for later # optionsStats <- analysis$optionsStats # # ## Change the directory back to the original one # setwd(initialPath) ## ----runDerfinderReal------------------------------------------------------------------------------------------------- ## Copy previous results file.copy(system.file(file.path("extdata", "chr21"), package = "derfinder", mustWork = TRUE ), "derfinderReport-example", recursive = TRUE) ## ----mergeResults----------------------------------------------------------------------------------------------------- ## Merge the results from the different chromosomes. In this case, there's ## only one: chr21 mergeResults( chrs = "chr21", prefix = "derfinderReport-example", genomicState = genomicState$fullGenome ) ## Load optionsStats load(file.path("derfinderReport-example", "chr21", "optionsStats.Rdata"), verbose = TRUE) ## ----loadLib, message=FALSE------------------------------------------------------------------------------------------- ## Load derfindeReport library("regionReport") ## ----createReport, eval = FALSE--------------------------------------------------------------------------------------- # ## Generate the HTML report # report <- derfinderReport( # prefix = "derfinderReport-example", browse = FALSE, # nBestRegions = 15, makeBestClusters = TRUE, # fullCov = list("21" = genomeDataRaw$coverage), optionsStats = optionsStats # ) ## ----vignetteBrowse, eval=FALSE--------------------------------------------------------------------------------------- # ## Browse the report # browseURL(report) ## ----createVignette, eval=FALSE--------------------------------------------------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("regionReport.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("regionReport.Rmd", tangle = TRUE) ## ----createVignette2-------------------------------------------------------------------------------------------------- ## Clean up unlink("derfinderReport-example", recursive = TRUE) ## ----vignetteReproducibility1, echo=FALSE----------------------------------------------------------------------------- ## Date the report was generated Sys.time() ## ----vignetteReproducibility2, echo=FALSE----------------------------------------------------------------------------- ## Processing time in seconds totalTimeVignette <- diff(c(startTimeVignette, Sys.time())) round(totalTimeVignette, digits = 3) ## ----vignetteReproducibility3, echo=FALSE----------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results='asis', echo=FALSE, warning = FALSE, message = FALSE------------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))