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Package Vignettes

Each Bioconductor package contains at least one vignette, a document that provides a task-oriented description of package functionality. Vignettes contain executable examples and are intended to be used interactively.

You can access the compiled version of a vignette for any installed package from inside R using the browseVignettes function. For example, to view the vignettes in the Biostrings package enter the following at an R prompt:

browseVignettes(package = "Biostrings")

This will open a web browser with links to the compiled vignette, as well as a plain-text R file containing the code used in the vignette.

The vignette files, both the compiled and the sources documents, are located in the doc directory of an installed package (inst/doc for an uninstalled package tarball). You can discover the location of an installed package as follows:

system.file(package = "Biostrings")

Older vignettes are mostly written in Sweave format with extension Rnw while newer vignttes mostly take advantage of Rmarkdown with extension Rmd. You can extract all of the R code from a vignette source file from a package. The result will be a .R file for each vignette source file written to your current working directory. You can use these R files to cut and paste into an R session so that you can work the examples in the vignette yourself.

The steps to extract R code depend if the source code is a Rnw Sweave format or Rmd Rmarkdown format. These commands would be run at an R prompt.

For Sweave we use tools::Stangle:

library("tools")
vigSrc = list.files(pattern = "Rnw$",
                    system.file("doc", package = "Biostrings"),
                    full.names = TRUE)
vigSrc
for (v in vigSrc) Stangle(v)

For Rmarkdown we use knitr::purl:

library("knitr")
vigSrc = list.files(pattern = "Rmd$",
                    system.file("doc", package = "BiocFileCache"),
                    full.names = TRUE)
vigSrc
for (v in vigSrc) purl(v)

You can also view or download the vignette for a package that isn’t installed on your system by visiting the package’s description page linked from the list of Bioconductor packages

Term of use for the vignettes: You are welcome to use these materials for instructional purposes. However, you may not include these in separately published works (articles, books, websites). When using all or parts of the Bioconductor course materials (slides, vignettes, scripts), we would appreciate it if you would cite the authors and refer your audience to the Bioconductor website.

Please also remember to check package documention help files. You can access help files for a package within R with ?.

library("Biostrings")
?DNAString
?reverseComplement