recommendBiocViews: Recommend biocViews for an existing Package.

In Bioconductor/biocViews: Categorized views of R package repositories

Recommend biocViews for an existing Package.

Description

Packages being added to the Bioconductor Project require biocViews in their DESCRIPTION file.(Note that the field name "biocViews" is case-sensitive and must begin with a lower-case 'b'.)biocViews are "keywords" which are used to describe a given package. They are broadly divided into three categories, representing the type of packages present in the Bioconductor Project - Software, Annotation Data and Experiment Data.

Usage

    recommendBiocViews(pkgdir, branch)

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'.

Details

This function parses the package directory provided by the user to recommend biocViews to the user. The output is a suggested list - the user of this function is expected to go through this list and find which biocViews best describe his or her package. It uses the following strategies.

• It parses the "Description", "Title", "Package" of the DESCRIPTION page to find biocViews.

• It looks up the biocViews of the packages in the "Depends" field of the given package to recommend biocViews

• It parses the text from the man pages and the vignettes to suggest biocViews.

Please note the following:

• Do not make up your own biocViews.

• Double check the spelling and case of the biocViews added.

• Please add biocViews only from the appropriate branch. eg: Software packages should have only Software biocViews.

Value

A list is returned with 3 characters - current , recommended and remove.

• "current" contains the biocViews from the package's DESCRIPTION file.

• "recommended" are the recommended biocViews - This is a suggested list which the user can add in addition to "current" biocViews - the user is expected to go through this list and find which biocViews best describe their package.

• "remove" are those biocViews which are inconsistent with the Bioconductor biocViews. (Hint - check for spelling, cases and plural)

Author(s)

Sonali Arora.

Bioconductor/biocViews documentation built on Nov. 2, 2024, 7:23 a.m.