## ----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 bib <- c( BiocStyle = citation("BiocStyle"), brainspan = RefManageR::BibEntry(bibtype = "Unpublished", key = "brainspan", title = "Atlas of the Developing Human Brain [Internet].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"), knitcitations = citation("knitcitations"), knitr = citation("knitr")[3], rmarkdown = citation("rmarkdown")[1] ) write.bibtex(bib, file = "derfinderDataRef.bib") ## ----'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'----------------------------------------- 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----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("derfinderData.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("derfinderData.Rmd", tangle = TRUE) ## ----createVignette2---------------------------------------------------------- ## Clean up file.remove("derfinderDataRef.bib") ## ----reproducibility1, echo=FALSE--------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproducibility2, echo=FALSE--------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproducibility3, echo=FALSE--------------------------------------------- ## Session info library("sessioninfo") session_info() ## ----vignetteBiblio, results='asis', echo=FALSE------------------------------- ## Print bibliography bibliography()