shared-upset

Shared parameters for upset functions

internal

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. 

shared-upset function

<dl><dt>anchor</dt>
<dd>The primary testID to filter the results</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>column</dt>
<dd>The columns to apply the filters</dd>
<dt>type</dt>
<dd>Type of p-value: (<code>"nominal"</code> or <code>"adjusted"</code>)</dd>
<dt>tests</dt>
<dd>Restrict UpSet plot to only include these tests</dd>
<dt>legacy</dt>
<dd>Use legacy code (for testing purposes only)</dd></dl>

Arguments

Shared parameters for upset functions — shared-upset

<dl>

<dt>anchor</dt>
<dd>The primary testID to filter the results</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>column</dt>
<dd>The columns to apply the filters</dd>


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


<dt>tests</dt>
<dd>Restrict UpSet plot to only include these tests</dd>


<dt>legacy</dt>
<dd>Use legacy code (for testing purposes only)</dd>

</dl>

Shared parameters for upset functions

shared-upset: Shared parameters for upset functions

Description

Arguments