weightedSetCover

Size constrained weighted set cover problem to find top N sets while
maximizing the coverage of all elements.

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

weightedSetCover function

<dl><dt>idsInSet</dt>
<dd>A list of set names and their member IDs.</dd>
<dt>costs</dt>
<dd>A vector of the same length to add weights for penalty, i.e. 1/-logP.</dd>
<dt>topN</dt>
<dd>The number of sets (or less when it completes early) to return.</dd>
<dt>nThreads</dt>
<dd>The number of processes to use. In Windows, it fallbacks to 1.</dd></dl>

Arguments

Author

Weighted Set Cover — weightedSetCover

<dl>

<dt>idsInSet</dt>
<dd>A list of set names and their member IDs.</dd>


<dt>costs</dt>
<dd>A vector of the same length to add weights for penalty, i.e. 1/-logP.</dd>


<dt>topN</dt>
<dd>The number of sets (or less when it completes early) to return.</dd>


<dt>nThreads</dt>
<dd>The number of processes to use. In Windows, it fallbacks to 1.</dd>

</dl>

weightedSetCover: Weighted Set Cover

Description

Usage

Value

Arguments

Author