AlvMac_GOgenes: Example of custom mapping between gene ontology identifiers...

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

Description

An example data.frame associating Ensembl gene identifiers to gene ontology identifiers, compatible with the AlvMac example ExpressionSet.

Usage

data("AlvMac_GOgenes")

Details

This data-frame includes all annotations between Ensembl gene identifiers and gene ontology identifiers present in the btaurus_gene_ensembl dataset of the Ensembl BioMart server, including gene identifiers absent from the AlvMac example ExpressionSet.

Importantly, gene identifiers present in these annotations but absent from the ExpressionSet will be given a score of 0 (minimum valid score; indicates no power to discriminates the predefined groups of sample) and a rank equal to the number of genes present in the entire dataset plus one (worst rank, while preserving discrete continuity of the ranking). This is helpful where features considered uninformative were filtered out of the ExpressionSet.

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

Value

A data frame with 191,614 associations between the following 2 variables.

• gene_id are Ensembl gene identifiers of the Bos taurus species.

• go_id are gene ontology identifiers.

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_GOgenes)

# Structure of the data
str(AlvMac_GOgenes)

# First few rows
head(AlvMac_GOgenes)

kevinrue/GOexpress-release documentation built on May 20, 2019, 9:08 a.m.