supportedOrganisms: Supported Organisms

In nadiadavidson/goseq: Gene Ontology analyser for RNA-seq and other length biased data

Description

Lists which genomes and gene ids are supported for gene lengths and for gene ontology

Usage

supportedOrganisms()

Details

Goseq allows a user to provide their own bias data (usually gene lengths) and/or gene categories (usually gene ontologies), but goseq also provides this data automatically for many commonly used species. This function lists which genome and gene ids are automatically supported by goseq. The first to third columns list the genomes, gene ids, and gene id descriptions respectively. The fourth column indicates whether this combination of genome and id are available in the geneLengthDataBase. If a particular combination is absent, goseq may still automatically fetch the gene lengths from either a TxDB annotation package (must be installed) or download the data from UCSC. For example gene lengths for hg38 are not supported in geneLengthDataBase but may be fetched by these other means. However, this is not always the case. The final column indicates if GO terms will be automatically fetched for the geneome and id combination. Goseq relies on an org annotation package (e.g. org.Hs.eg.db) existing for the organism. In general, if either the lengths or GO terms are not supported, the user must enter this information manually.

Value

A data.frame containing supported genomes and gene ids

Author(s)

Nadia Davidson [e-mail]

Examples

supportedOrganisms()

nadiadavidson/goseq documentation built on Oct. 28, 2019, 10:27 a.m.