## ----'installDer', eval = FALSE------------------------------------------ # ## try http:// if https:// URLs are not supported # source("https://bioconductor.org/biocLite.R") # biocLite("regionReport") # # ## Check that you have a valid Bioconductor installation # biocValid() ## ----'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('knitcitations') ## Load knitcitations with a clean bibliography cleanbib() cite_options(hyperlink = 'to.doc', citation_format = 'text', style = 'html') # Note links won't show for now due to the following issue # https://github.com/cboettig/knitcitations/issues/63 ## Write bibliography information bibs <- c(knitcitations = citation('knitcitations'), derfinder = citation('derfinder')[1], regionReport = citation('regionReport')[1], knitrBootstrap = citation('knitrBootstrap'), #BiocStyle = citation('BiocStyle'), BiocStyle = RefManageR::BibEntry(bibtype = 'unpublished', key = 'BiocStyle', title = 'BiocStyle: Standard styles for vignettes and other Bioconductor documents', author = 'Martin Morgan and Andrzej OleÅ› and Wolfgang Huber', note = 'R package version 1.8.0', year = '2015'), ggbio = citation('ggbio'), ggplot2 = citation('ggplot2'), knitr = citation('knitr')[3], rmarkdown = citation('rmarkdown'), DT = citation('DT'), R = citation(), IRanges = citation('IRanges'), devtools = citation('devtools'), #GenomeInfoDb = citation('GenomeInfoDb'), GenomeInfoDb = RefManageR::BibEntry(bibtype = 'unpublished', key = 'GenomeInfoDb', title = "GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers", author = 'Sonali Arora and Martin Morgan and Marc Carlson and H. Pages', note = 'R package version 1.7.3', year = '2015'), GenomicRanges = citation('GenomicRanges'), #biovizBase = citation('biovizBase'), biovizBase = RefManageR::BibEntry(bibtype = 'unpublished', key = 'biovizBase', title = 'biovizBase: Basic graphic utilities for visualization of genomic data.', author = 'Tengfei Yin and Michael Lawrence and Dianne Cook', note = 'R package version 1.19.0', year = '2015'), #TxDb.Hsapiens.UCSC.hg19.knownGene = citation('TxDb.Hsapiens.UCSC.hg19.knownGene'), TxDb.Hsapiens.UCSC.hg19.knownGene = RefManageR::BibEntry(bibtype = 'unpublished', key = 'TxDb.Hsapiens.UCSC.hg19.knownGene', title = 'TxDb.Hsapiens.UCSC.hg19.knownGene: Annotation package for TxDb object(s)', author = 'Marc Carlson and Bioconductor Package Maintainer', note = 'R package version 3.2.2', year = '2015'), derfinderPlot = citation('derfinderPlot')[1], grid = citation('grid'), gridExtra = citation('gridExtra'), mgcv = citation('mgcv'), RColorBrewer = citation('RColorBrewer'), Cairo = citation('Cairo'), whikser = citation('whisker'), bumphunter = citation('bumphunter')[1], pheatmap = citation('pheatmap'), DESeq2 = citation('DESeq2'), edgeR1 = citation('edgeR')[1], edgeR2 = citation('edgeR')[2], edgeR5 = citation('edgeR')[5], 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') ) write.bibtex(bibs, file = 'regionReportRef.bib') bib <- read.bibtex('regionReportRef.bib') ## Assign short names names(bib) <- names(bibs) ## ---- 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 'report' directory dir.create('report', showWarnings = FALSE, recursive = TRUE) ## ----runDerfinderFake, eval=FALSE---------------------------------------- # ## Save the current path # initialPath <- getwd() # setwd(file.path(initialPath, 'report')) # # ## 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), 'report', recursive=TRUE) ## ----mergeResults-------------------------------------------------------- ## Merge the results from the different chromosomes. In this case, there's ## only one: chr21 mergeResults(chrs = 'chr21', prefix = 'report', genomicState = genomicState$fullGenome) ## Load optionsStats load(file.path('report', 'chr21', 'optionsStats.Rdata')) ## ----loadLib, message=FALSE---------------------------------------------- ## Load derfindeReport library('regionReport') ## ----createReport-------------------------------------------------------- ## Generate the HTML report report <- derfinderReport(prefix='report', browse=FALSE, nBestRegions=15, makeBestClusters=TRUE, outdir='html', fullCov=list('21'=genomeDataRaw$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 file.remove('regionReportRef.bib') unlink('report', 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('devtools') options(width = 120) session_info() ## ----vignetteBiblio, results='asis', echo=FALSE, warning = FALSE------------------------------------------------------ ## Print bibliography bibliography()