Infer biocViews — infer_biocviews • rworkflows

Infer the best terms to fill the biocViews field in your DESCRIPTION file based on the code within your R package. By default, also includes any biocViews that are already present in the DESCRIPTION file. Please see the Bioconductor website for more details.

infer_biocviews(
  pkgdir = here::here(),
  branch = c("Software", "AnnotationData", "ExperimentData")[1],
  type = c("recommended", "current", "remove"),
  keep_current = TRUE,
  include_branch = TRUE,
  biocviews = NULL,
  add_newlines = FALSE,
  verbose = TRUE
)

Arguments

pkgdir: The path of the package Directory.
branch: The branch which your package will belong to. It can be either 'Software', 'AnnotationData' or 'ExperimentData'.
type: Which element of the recommendBiocViews results list to return. If a vector is supplied, only the first value will be used.
keep_current: Keep any biocViews terms that are already included in the DESCRIPTION file.
include_branch: Whether to include the branch argument as one of the returned biocViews.
biocviews: User-supplied biocViews terms to include in addition to the automated recommendations.
add_newlines: Prefix each package name with a newline character and two spaces. This is useful for formatting DESCRIPTION files.
verbose: Print messages.

Value

A character vector of biocviews.

Examples

## Don't run simply bc biocViews::recommendBiocViews is unable 
## to find the DESCRIPTION file when running examples.
if (FALSE) {
biocviews <- infer_biocviews()
}