prefix2dataset: Table mapping Ensembl gene identifier prefixes to BioMart...

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

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

kevinrue/GOexpress documentation built on May 19, 2020, 7:23 p.m.