listReferenceSet

List available reference sets for the given organism on WebGestalt server.

The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

Yuxing Liao

WebGestaltR

Gene Set Analysis Toolkit WebGestaltR

Jing Wang

Eric Jaehnig

Zhiao Shi

Quanhu Sheng

listReferenceSet function

<dl><dt>organism</dt>
<dd>Currently, WebGestaltR supports 12 organisms. Users can use the function
<code>listOrganism</code> to check available organisms. Users can also input <code>others</code> to
perform the enrichment analysis for other organisms not supported by WebGestaltR. For
other organisms, users need to provide the functional categories, interesting list and
reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for
the other organisms, the above data should have the same ID type.</dd>
<dt>hostName</dt>
<dd>The server URL for accessing data. Mostly for development purposes.</dd>
<dt>cache</dt>
<dd>A directory to save data cache for reuse. Defaults to <code>NULL</code> and disabled.</dd></dl>

Arguments

List Reference Sets — listReferenceSet

<dl>

<dt>organism</dt>
<dd>Currently, WebGestaltR supports 12 organisms. Users can use the function
<code>listOrganism</code> to check available organisms. Users can also input <code>others</code> to
perform the enrichment analysis for other organisms not supported by WebGestaltR. For
other organisms, users need to provide the functional categories, interesting list and
reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for
the other organisms, the above data should have the same ID type.</dd>


<dt>hostName</dt>
<dd>The server URL for accessing data. Mostly for development purposes.</dd>


<dt>cache</dt>
<dd>A directory to save data cache for reuse. Defaults to <code>NULL</code> and disabled.</dd>

</dl>

listReferenceSet: List Reference Sets

Description

Usage

Value

Arguments