infer_biocviews: Infer biocViews

In rworkflows: Test, Document, Containerise, and Deploy R Packages

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)

rworkflows documentation built on Sept. 23, 2024, 1:08 a.m.