table_genes {GOexpress} | R Documentation |
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.
table_genes(go_id, result, data.only=FALSE, order.by='rank')
go_id |
A Gene Ontology (GO) identifier. |
result |
The output of the |
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')