## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle"), derfinder = citation("derfinder")[1], derfinderPlot = citation("derfinderPlot")[1], sessioninfo = citation("sessioninfo"), GenomicRanges = citation("GenomicRanges"), knitr = citation("knitr")[3], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], rtracklayer = citation("rtracklayer"), testthat = citation("testthat"), ggplot2 = citation("ggplot2"), cowplot = citation("cowplot"), BSgenome.Hsapiens.UCSC.hg19 = citation("BSgenome.Hsapiens.UCSC.hg19"), Biostrings = citation("Biostrings"), RColorBrewer = citation("RColorBrewer"), bumphunter = citation("bumphunter")[1], GenomicState = citation("GenomicState") ) ## ----'install', eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("brainflowprobes") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() # # ## If you want to force the installation of the development version, you can # ## do so by running. However, we suggest that you wait for Bioconductor to # ## run checks and build the latest release. # BiocManager::install("LieberInstitute/brainflowprobes") ## ----'citation'--------------------------------------------------------------- ## Citation info citation("brainflowprobes") ## ----'start', message=FALSE--------------------------------------------------- ## Load brainflowprobes R package library("brainflowprobes") ## ----'annotate'--------------------------------------------------------------- region_info("chr2:162279880-162282378:+", CSV = FALSE, SEQ = TRUE, OUTDIR = ".") ## ----'visualize coverage', eval = FALSE--------------------------------------- # plot_coverage("chr2:162279880-162282378:+", # PDF = "regionCoverage_fractionedData.pdf", # OUTDIR = ".", # COVERAGE = NULL, VERBOSE = FALSE # ) ## ---- include=TRUE, fig.align="center", echo=FALSE, out.height = 850---------- knitr::include_graphics("regionCoverage_fractionedData.pdf") ## ----'visualize shorter region coverage', eval = FALSE------------------------ # plot_coverage("chr2:162280900-162282378:+", # PDF = "regionCoverage_fractionedData_shorter.pdf", # OUTDIR = ".", # COVERAGE = NULL, VERBOSE = FALSE # ) ## ---- include=TRUE, fig.align="center", echo=FALSE, out.height = 850---------- knitr::include_graphics("regionCoverage_fractionedData_shorter.pdf") ## ----'precalculate coverage', eval = FALSE------------------------------------ # tbr1.cov <- brainflowprobes_cov("chr2:162280900-162282378:+", VERBOSE = FALSE) ## ----'plot four panels', eval = FALSE----------------------------------------- # four_panels("chr2:162280900-162282378:+", # PDF = "four_panels.pdf", # OUTDIR = ".", # JUNCTIONS = FALSE, # COVERAGE = tbr1.cov, VERBOSE = FALSE # ) ## ---- include=TRUE, fig.align="center", echo=FALSE, out.height = 1000--------- knitr::include_graphics("four_panels.pdf") ## ----'annotate multiple'------------------------------------------------------ candidates <- c( "chr2:162279880-162282378:+", "chr11:31806351-31811553", "chr7:103112236-103113354" ) region_info(candidates, CSV = FALSE, SEQ = FALSE) ## ----'plot multiple', eval=FALSE---------------------------------------------- # plot_coverage(candidates, # PDF = "regionCoverage_fractionedData_multiple.pdf", OUTDIR = "." # ) # # four_panels(candidates, PDF = "four_panels_multiple.pdf", OUTDIR = ".") ## ----'PENK', eval=FALSE------------------------------------------------------- # PENK_exons <- c( # "chr8:57353587-57354496:-", # "chr8:57358375-57358515:-", # "chr8:57358985-57359040:-", # "chr8:57359128-57359292:-" # ) # # four_panels(PENK_exons, JUNCTIONS = TRUE, PDF = "PENK_panels.pdf") ## ----createVignette, eval=FALSE----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("brainflowprobes-vignette.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("brainflowprobes-vignette.Rmd", tangle = TRUE) ## ----reproduce1, echo=FALSE--------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE--------------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproduce3, 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"))