GeneSet-class: Class '"GeneSet"'

In sartorlab/chipenrich.data: Companion package to chipenrich

Class "GeneSet"

Description

Class for storing sets of genes and their corresponding metadata.

Objects from the Class

Objects can be created by calls of the form new("GeneSet").

These objects are used internally by the chipenrich package and users will not likely need to create these.

Slots

set.gene:

Object of class "environment". Maps from geneset IDs to lists of Entrez gene IDs.

type:

Object of class "character". The formal name for this collection of genesets.

set.name:

Object of class "environment". Maps from geneset IDs to their descriptions/names.

all.genes:

Object of class "character". A set of all genes present across every geneset.

organism:

Object of class "character". Organism code for gene IDs.

dburl:

Object of class "character". Web URL for this collection of genesets.

Note

Not typically accessed by the user - this is used internally by the chipenrich package.

Author(s)

Ryan Welch [e-mail]

Examples

# Show information about class.
showClass("GeneSet")

# What is stored inside a geneset object?
data("geneset.metabolite.hsa");
str(geneset.metabolite.hsa);

# How are the mappings from geneset IDs to gene IDs stored?
ls.str([e-mail]);

sartorlab/chipenrich.data documentation built on Oct. 4, 2023, 5:21 p.m.