AlvMac_GOgenes {GOexpress} | R Documentation

## Example of custom mapping between gene ontology identifiers and gene features.

### 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)

[Package GOexpress version 1.20.0 Index]