table_genes: Returns a table listing the genes associated with a given...
In GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`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.

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

Kevin Rue-Albrecht

Method GO_analyse.

# 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')