prefix2dataset {GOexpress} | R Documentation

## Table mapping Ensembl gene identifier prefixes to BioMart datasets.

### Description

The species corresponding to an Ensembl gene identifier can typically be identified from the prefix of the identifier (e.g. ENSBTAG corresponds to Bos taurus). This table maps each known unique prefix to the corresponding species.

### Usage

    data(prefix2dataset)

### Details

C. elegans, D. melanogaster, and S. cerevisiae have atypical identifier pattern and prefixes in their Ensembl gene identifiers. However, the automatically extracted prefix for C. elegans and D. melanogaster – respectively "WBgene" and "FBgn" – can be used as such to identify datasets from those species. On the oher hand, prefixes used for the S. cerevisiae include "YHR", "YAL", and many others. Consequently, expression data from S. cerevisiae species is identified without referring to the "prefix2dataset"" table; instead, such datasets are identified if the first gene identifier in the dataset starts with "Y".

### Value

A data frame with 69 rows and 4 columns. Each row refers to one dataset in the Ensembl BioMart. The columns are described below:

- `dataset` contains the biomaRt dataset name.

- `species` contains the corresponding species name.

- `prefix` contains the corresponding unique prefix.

- `sample` contains a sample Ensembl gene identifier from this dataset.

### Source

The `prefix2dataset.build` method stored in the `toolkit.R` script was used to query the Ensembl BioMart server and build this table.

### Examples

    data(prefix2dataset)
    str(prefix2dataset)
    prefix2dataset

[Package GOexpress version 1.20.0 Index]