annotation: annotation class

In MoseleyBioinformaticsLab/categoryCompare2: Meta-Analysis of High-Throughput Experiments Using Feature Annotations

annotation class

Description

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 signature '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

MoseleyBioinformaticsLab/categoryCompare2 documentation built on Nov. 3, 2024, 11:06 a.m.