infer_biocviews {rworkflows}

Infer biocViews

Description

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.

Usage

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.
## Not run: 
biocviews <- infer_biocviews()

## End(Not run)