## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL #https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----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")[1], knitr = citation("knitr")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], GSE159526 = citation("GSE159526")[1] ) ## ----"citation"--------------------------------------------------------------- ## Citation info citation("GSE159526") ## ----"start", message=FALSE, eval=FALSE--------------------------------------- # eh <- ExperimentHub() # query(eh, "GSE159526") # # # raw rgset # library(minfi) # GSE159526_rgset <- eh[['EH6130']] # requires minfi # # # normalized processed data matrix # GSE159526_data <- eh[['EH6131']] # # # sample information # GSE159526_pdat <- eh[['EH6132']] ## ----createVignette, eval=FALSE----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render(here::here("vignettes", "GSE159526.Rmd"), # "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("GSE159526.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"))