table_genes: Returns a table listing the genes associated with a given...

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

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')

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