getEnsemblGeneIds

Not exported to avoid unintended modifications of the DB.

An interface for the 'Neo4j' database providing
mapping between different identifiers of biological entities.
This Biological Entity Dictionary (BED)
has been developed to address three main challenges.
The first one is related to the completeness of identifier mappings.
Indeed, direct mapping information provided by the different systems
are not always complete and can be enriched by mappings provided by other
resources.
More interestingly, direct mappings not identified by any of these
resources can be indirectly inferred by using mappings to a third reference.
For example, many human Ensembl gene ID are not directly mapped to any
Entrez gene ID but such mappings can be inferred using respective mappings
to HGNC ID. The second challenge is related to the mapping of deprecated
identifiers. Indeed, entity identifiers can change from one resource
release to another. The identifier history is provided by some resources,
such as Ensembl or the NCBI, but it is generally not used by mapping tools.
The third challenge is related to the automation of the mapping process
according to the relationships between the biological entities of interest.
Indeed, mapping between gene and protein ID scopes should not be done
the same way than between two scopes regarding gene ID.
Also, converting identifiers from different organisms should be possible
using gene orthologs information.
The method has been published by
Godard and van Eyll (2018) <doi:10.12688/f1000research.13925.3>.

Patrice Godard

Biological Entity Dictionary (BED)

getEnsemblGeneIds function

<dl><dt>organism</dt>
<dd>character vector of 1 element corresponding to the organism
of interest (e.g. "Homo sapiens")</dd>
<dt>release</dt>
<dd>the Ensembl release of interest (e.g. "83")</dd>
<dt>gv</dt>
<dd>the genome version (e.g. "38")</dd>
<dt>ddir</dt>
<dd>path to the directory where the data should be saved</dd>
<dt>dbCref</dt>
<dd>a named vector of characters providing cross-reference DB of
interest. These DB are also used to find indirect ID associations.</dd>
<dt>dbAss</dt>
<dd>a named vector of characters providing associated DB of
interest. Unlike the DB in dbCref parameter, these DB are not used for
indirect ID associations: the IDs are only linked to Ensembl IDs.</dd>
<dt>canChromosomes</dt>
<dd>canonical chromosmomes to be considered as preferred
ID (e.g. c(1:22, "X", "Y", "MT") for human)</dd></dl>

Arguments

Feeding BED: Download Ensembl DB and load gene information in BED — getEnsemblGeneIds

<dl>

<dt>organism</dt>
<dd>character vector of 1 element corresponding to the organism
of interest (e.g. "Homo sapiens")</dd>


<dt>release</dt>
<dd>the Ensembl release of interest (e.g. "83")</dd>


<dt>gv</dt>
<dd>the genome version (e.g. "38")</dd>


<dt>ddir</dt>
<dd>path to the directory where the data should be saved</dd>


<dt>dbCref</dt>
<dd>a named vector of characters providing cross-reference DB of
interest. These DB are also used to find indirect ID associations.</dd>


<dt>dbAss</dt>
<dd>a named vector of characters providing associated DB of
interest. Unlike the DB in dbCref parameter, these DB are not used for
indirect ID associations: the IDs are only linked to Ensembl IDs.</dd>


<dt>canChromosomes</dt>
<dd>canonical chromosmomes to be considered as preferred
ID (e.g. c(1:22, "X", "Y", "MT") for human)</dd>

</dl>

getEnsemblGeneIds: Feeding BED: Download Ensembl DB and load gene information in BED

Description

Usage

Arguments