AlvMac_allGO: Example of custom gene ontology annotations.

In kevinrue/GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

Description

An example data.frame providing the identifier, name and namespace corresponding to gene ontology identifiers, compatible with the AlvMac example ExpressionSet.

Usage

data("AlvMac_allGO")

Details

This data-frame includes all gene ontologies present in the btaurus_gene_ensembl dataset of the Ensembl BioMart server, including those associated with no gene identifier in the AlvMac example ExpressionSet.

See the help page of the GO_analyse function for an example usage.

Value

A data frame detailing information about 13,302 gene ontologies:

• go_id are gene ontology identifiers.

• name_1006 contains the corresponding gene ontology name.

• namespace_1003 contains the corresponding gene ontology namespace (i.e. "biological_process", "molecular_function", or "cellular_component")

Source

These annotations were obtained from the Ensembl BioMart server using the biomaRt package to access the Ensembl release 75 http://feb2014.archive.ensembl.org.

Examples

# Load the data
data(AlvMac_allGO)

# Structure of the data
str(AlvMac_allGO)

# First few rows
head(AlvMac_allGO)

kevinrue/GOexpress documentation built on May 19, 2020, 7:23 p.m.