getEnrichmentsIntersection

A tool for interactive exploration of the results from 'omics'
experiments to facilitate novel discoveries from high-throughput biology. The
software includes R functions for the 'bioinformatician' to deposit study
metadata and the outputs from statistical analyses (e.g. differential
expression, enrichment). These results are then exported to an interactive
JavaScript dashboard that can be interrogated on the user's local machine or
deployed online to be explored by collaborators. The dashboard includes
'sortable' tables, interactive plots including network visualization, and
fine-grained filtering based on statistical significance.

John Blischak

OmicNavigator

Open-Source Software for 'Omic' Data Analysis and Visualization

Terrence Ernst

Paul Nordlund

Justin Moore

Joe Dalen

Akshay Bhamidipati

Brett Engelmann

Marco Curado

Joe LoGrasso

AbbVie Inc. 

getEnrichmentsIntersection function

<dl><dt>study</dt>
<dd>An OmicNavigator study. Either an object of class <code>onStudy</code>,
or the name of an installed study package.</dd>
<dt>modelID</dt>
<dd>Filter by modelID</dd>
<dt>annotationID</dt>
<dd>Filter by annotationID</dd>
<dt>mustTests</dt>
<dd>The testIDs for which a featureID (or termID for enrichment)
must pass the filters</dd>
<dt>notTests</dt>
<dd>The testIDs for which a featureID (or termID for enrichment)
must not pass the filters. In other words, if a featureID passes the
filter for a testID specified in notTests, that featureID is removed from
the output</dd>
<dt>sigValue</dt>
<dd>The numeric significance value to use as a cutoff for each
column</dd>
<dt>operator</dt>
<dd>The comparison operators for each column, e.g. <code>"&lt;"</code></dd>
<dt>type</dt>
<dd>Type of p-value: (<code>"nominal"</code> or <code>"adjusted"</code>)</dd></dl>

Arguments

getEnrichmentsIntersection — getEnrichmentsIntersection

<dl>

<dt>study</dt>
<dd>An OmicNavigator study. Either an object of class <code>onStudy</code>,
or the name of an installed study package.</dd>


<dt>modelID</dt>
<dd>Filter by modelID</dd>


<dt>annotationID</dt>
<dd>Filter by annotationID</dd>


<dt>mustTests</dt>
<dd>The testIDs for which a featureID (or termID for enrichment)
must pass the filters</dd>


<dt>notTests</dt>
<dd>The testIDs for which a featureID (or termID for enrichment)
must not pass the filters. In other words, if a featureID passes the
filter for a testID specified in notTests, that featureID is removed from
the output</dd>


<dt>sigValue</dt>
<dd>The numeric significance value to use as a cutoff for each
column</dd>


<dt>operator</dt>
<dd>The comparison operators for each column, e.g. <code>"&lt;"</code></dd>


<dt>type</dt>
<dd>Type of p-value: (<code>"nominal"</code> or <code>"adjusted"</code>)</dd>

</dl>

getEnrichmentsIntersection: getEnrichmentsIntersection

Description

Usage

Value

Arguments

See Also