annotation class — annotation • categoryCompare2

This class holds an annotation object that defines how annotations relate to features, as well as various pieces about each annotation

Does sensical checks when creating an annotation object.

Usage

annotation(
  annotation_features,
  annotation_type = NULL,
  description = character(0),
  links = character(0),
  feature_type = NULL
)

# S4 method for class 'annotation'
show(object)

annotation(
  annotation_features,
  annotation_type = NULL,
  description = character(0),
  links = character(0),
  feature_type = NULL
)

Arguments

annotation_features: list of annotation to feature relationships
annotation_type: a simple one word description of the annotations
description: character vector providing descriptive text about the annotation
links: character vector defining html links for each annotation (may be empty)
feature_type: one word description of the feature type
object: the annotation object

Details

These objects may be created by hand, or may result from specific functions to create them. Most notably, this package provides functions for creating a Gene Ontology annotation.

See the annotation, each slot is a parameter.

Slots

annotation_features: list of annotation to feature relationships
description: character vector providing descriptive text about the annotation
counts: numeric vector of how many features are in each annotation
links: character vector defining html links for each annotation (may be empty)
annotation_type: a one word short description of the "type" of annotation
feature_type: a one word short description of the "type" of features