annotatr_cache: A global-variable to hold custom annotations loaded in an R...

In rcavalcante/annotatr: Annotation of Genomic Regions to Genomic Annotations

A global-variable to hold custom annotations loaded in an R session

Description

Code thanks to Martin Morgan. This is a global variable that will store custom annotations that a user reads in during a session in which annotatr is loaded.

Usage

annotatr_cache

Format

An object of class list of length 3.

Value

An environment to contain custom annotations from read_annotations.

Examples

 # Example usage
 annotatr_cache$set("foo", 1:10)
 annotatr_cache$get("foo")

 # Read in a BED3 file as a custom annotation
 file = system.file('extdata', 'test_annotations_3.bed', package='annotatr')
 # The custom annotation is added to the annotatr_cache environment in this function
 read_annotations(con = file, name = 'test', genome = 'hg19')
 # The result of read_annotations() is not visible in .GlobalEnv, instead
 # need to use the get method
 print(annotatr_cache$get('hg19_custom_test'))
 # See what is in the annotatr_cache
 annotatr_cache$list_env()

rcavalcante/annotatr documentation built on Aug. 22, 2024, 7:33 a.m.