## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE----------- ## Track time spent on making the vignette startTime <- 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information write.bibtex(c(knitcitations = citation('knitcitations'), brainspan = RefManageR::BibEntry(bibtype = 'Unpublished', key = 'brainspan', title = 'Atlas of the Developing Human Brain [Internet]. Funded by ARRA Awards 1RC2MH089921-01, 1RC2MH090047-01, and 1RC2MH089929-01.', author = 'BrainSpan', year = 2011, url = 'http://developinghumanbrain.org'), knitrBootstrap = citation('knitrBootstrap'), knitr = citation('knitr')[3], rmarkdown = citation('rmarkdown')), file = 'derfinderDataRef.bib') bib <- read.bibtex('derfinderDataRef.bib') ## Assign short names names(bib) <- c('knitcitations', 'brainspan', 'knitrBootstrap', 'knitr', 'rmarkdown') ## ----'pheno'------------------------------------------------------------- ## Construct brainspanPheno table brainspanPheno <- data.frame( gender = c('F', 'M', 'M', 'M', 'F', 'F', 'F', 'M', 'F', 'M', 'M', 'F', 'M', 'M', 'M', 'M', 'F', 'F', 'F', 'M', 'F', 'M', 'M', 'F'), lab = c('HSB97.AMY', 'HSB92.AMY', 'HSB178.AMY', 'HSB159.AMY', 'HSB153.AMY', 'HSB113.AMY', 'HSB130.AMY', 'HSB136.AMY', 'HSB126.AMY', 'HSB145.AMY', 'HSB123.AMY', 'HSB135.AMY', 'HSB114.A1C', 'HSB103.A1C', 'HSB178.A1C', 'HSB154.A1C', 'HSB150.A1C', 'HSB149.A1C', 'HSB130.A1C', 'HSB136.A1C', 'HSB126.A1C', 'HSB145.A1C', 'HSB123.A1C', 'HSB135.A1C'), Age = c(-0.442307692307693, -0.365384615384615, -0.461538461538461, -0.307692307692308, -0.538461538461539, -0.538461538461539, 21, 23, 30, 36, 37, 40, -0.519230769230769, -0.519230769230769, -0.461538461538461, -0.461538461538461, -0.538461538461539, -0.519230769230769, 21, 23, 30, 36, 37, 40) ) brainspanPheno$structure_acronym <- rep(c('AMY', 'A1C'), each = 12) brainspanPheno$structure_name <- rep(c('amygdaloid complex', 'primary auditory cortex (core)'), each = 12) brainspanPheno$file <- paste0('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/', brainspanPheno$lab, '.bw') brainspanPheno$group <- factor(ifelse(brainspanPheno$Age < 0, 'fetal', 'adult'), levels = c('fetal', 'adult')) ## ----'savePheno', eval = FALSE------------------------------------------- # ## Save pheno table # save(brainspanPheno, file = 'brainspanPheno.RData') ## ----'explorePheno', results = 'asis', bootstrap.show.code = FALSE------- library('knitr') ## Explore pheno p <- brainspanPheno[, -which(colnames(brainspanPheno) %in% c('structure_acronym', 'structure_name', 'file'))] kable(p, format = 'html', row.names = TRUE) ## ----'verifyPheno'------------------------------------------------------- ## Rename our newly created pheno data newPheno <- brainspanPheno ## Load the included data library('derfinderData') ## Verify identical(newPheno, brainspanPheno) ## ----'getData', eval = FALSE--------------------------------------------- # library('derfinder') # # ## Determine the files to use and fix the names # files <- brainspanPheno$file # names(files) <- gsub('.AMY|.A1C', '', brainspanPheno$lab) # # ## Load the data # system.time(fullCovAMY <- fullCoverage( # files = files[brainspanPheno$structure_acronym == 'AMY'], chrs = 'chr21')) # #user system elapsed # #4.505 0.178 37.676 # system.time(fullCovA1C <- fullCoverage( # files = files[brainspanPheno$structure_acronym == 'A1C'], chrs = 'chr21')) # #user system elapsed # #2.968 0.139 27.704 # # ## Write BigWig files # dir.create('AMY') # system.time(createBw(fullCovAMY, path = 'AMY', keepGR = FALSE)) # #user system elapsed # #5.749 0.332 6.045 # dir.create('A1C') # system.time(createBw(fullCovA1C, path = 'A1C', keepGR = FALSE)) # #user system elapsed # #5.025 0.299 5.323 # # ## Check that 12 files were created in each directory # all(c(length(dir('AMY')), length(dir('A1C'))) == 12) # #TRUE # # ## Save data for examples running on Windows # save(fullCovAMY, file = 'fullCovAMY.RData') # save(fullCovA1C, file = 'fullCovA1C.RData') ## ----'findData'---------------------------------------------------------- ## Find AMY BigWigs dir(system.file('extdata', 'AMY', package = 'derfinderData')) ## Find A1C BigWigs dir(system.file('extdata', 'A1C', package = 'derfinderData')) ## ----createVignette, eval=FALSE, bootstrap.show.code=FALSE--------------- # ## Create the vignette # library('knitrBootstrap') # # knitrBootstrapFlag <- packageVersion('knitrBootstrap') < '1.0.0' # if(knitrBootstrapFlag) { # ## CRAN version # library('knitrBootstrap') # system.time(knit_bootstrap('derfinderData.Rmd', chooser=c('boot', # 'code'), show_code = TRUE)) # unlink('derfinderData.md') # } else { # ## GitHub version # library('rmarkdown') # system.time(render('derfinderData.Rmd', # 'knitrBootstrap::bootstrap_document')) # } # ## Note: if you prefer the knitr version use: # # library('rmarkdown') # # system.time(render('derfinder.Rmd', 'html_document')) # # ## Extract the R code # library('knitr') # knit('derfinderData.Rmd', tangle = TRUE) # # ## Clean up # file.remove('derfinderDataRef.bib') ## ----reproducibility1, echo=FALSE, bootstrap.show.code=FALSE------------- ## Date the vignette was generated Sys.time() ## ----reproducibility2, echo=FALSE, bootstrap.show.code=FALSE------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits=3) ## ----reproducibility3, echo=FALSE, bootstrap.show.code=FALSE, bootstrap.show.message=FALSE---- ## Session info library('sessioninfo') session_info() ## ----vignetteBiblio, results='asis', echo=FALSE-------------------------- ## Print bibliography bibliography()