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 PDF version of a vignette for any installed package from inside R as follows:
library("Biobase")
## now load package of interset, here GOstats
library("GOstats")
openVignette()
This will present you with a menu where you can select the desired vignette. Selecting a vignette should cause the corresponding PDF file to open on your system.
The vignette files, both the PDF and the Rnw sources
document, 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 = "GOstats")
You can extract all of the R code from a vignette
source file (these files are in Sweave format) as shown
below. 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.
library("tools")
vigSrc = list.files(pattern = "Rnw$",
system.file("doc", package = "GOstats"),
full.names = TRUE)
vigSrc
for (v in vigSrc) Stangle(v)
You can also download the vignette for a package that isn't installed on your system. Package vignettes are linked from each package's description page which can be reached from the BiocViews page.
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