table_genes {GOexpress} | R Documentation

## Returns a table listing the genes associated with a given Gene Ontology

### Description

Given a Gene Ontology (GO) identifier represented in the dataset and the output variable of a `GO_analyse()` function, `table_genes()` returns a table listing the genes associated with that go_id, their associated gene name, and description.

### Usage

    table_genes(go_id, result, data.only=FALSE, order.by='rank')

### Arguments

`go_id` | A Gene Ontology (GO) identifier.
`result` | The output of the `GO_analyse()` function.
`data.only` | Whether to return only the feature identifiers present in the given dataset or alternatively returns all feature identifiers associated with the GO term in the Ensembl BioMart.
`order.by` | The metric or name to order the output table. Default is increasing 'rank', which corresponds to decreasing score. Valid values are 'rank' (increasing) equivalent to 'score' (decreasing), 'gene_id', 'name', equivalent to 'external_gene_name' and 'external_gene_id'. Text ranking in alphabetical order.

### Value

A data frame listing the statistics and annotations for the genes present in the expression dataset and associated with the GO term.

### Author(s)

Kevin Rue-Albrecht

### See Also

Method `GO_analyse`.

### Examples

    # load the sample output data
    data(AlvMac_results)

    # Table of result for genes associated with the GO term
    # "toll-like receptor 4 signaling pathway"
    table_genes(result=AlvMac_results, go_id="GO:0034142")

    # ordered by gene name
    table_genes(result=AlvMac_results, go_id="GO:0034142", order.by='name')

[Package GOexpress version 1.24.0 Index]