getBiocSubViews: Build a list of BiocView objects from a package repository
In biocViews: Categorized views of R package repositories

Description Usage Arguments Details Value Author(s) See Also Examples

This function returns a list of BiocView-class objects corresponding to the subgraph of the views DAG induced by topTerm. In short, this does the same thing as getBiocViews, but limits the vocabulary to topTerm and all of its decendents.

1	getBiocSubViews(reposUrl, vocab, topTerm, local = FALSE, htmlDir = "")

`reposUrl`	URL for a CRAN-style repository that hosts a `VIEWS` file at the top-level.
`vocab`	A `graph-class` object representing the ontologyof views. This graph should be a directed acyclic graph (DAG).
`topTerm`	A string giving the name of the subview DAG. This view and all of its decendents will be included in the result.
`local`	logical indicating whether to assume a local package repository. The default is `FALSE` in which case absolute links to package detail pages are created.
`htmlDir`	if the `local` argument is `TRUE`, this will be used as the relative path for package HTML files.

The root of the vocabulary DAG is implicitly included in the view creation process order to build views with a link back to the top. It is removed from the return list.

This function is tailored to generation of Bioconductor Task Views. With the current vocabulary, it probably only makes sense to call it with topView set to one of "Software", "AnnotationData", or "ExperimentData". This is a hack to allow the biocViews code to manage HTML views across more than one repository.

A list of BiocView-class objects. The names of the list give the name of the corresponding view.

Seth Falcon

write_VIEWS, writeBiocViews

data(biocViewsVocab)
reposPath <- system.file("doc", package="biocViews")
reposUrl <- paste("file://", reposPath, sep="")
biocViews <- getBiocSubViews(reposUrl, biocViewsVocab, "Software")
print(biocViews[1:2])