getEnrichmentsTable

Get enrichments table from a study

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. 

getEnrichmentsTable 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>type</dt>
<dd>Type of p-value: (<code>"nominal"</code> or <code>"adjusted"</code>)</dd>
<dt>libraries</dt>
<dd>The directories to search for installed study packages. If
left as <code>NULL</code> (the default), then
<code><a href="/link/installed.packages?package=OmicNavigator&version=1.13.13" data-mini-rdoc="OmicNavigator::installed.packages">installed.packages</a></code> will use the result of
<code><a href="/link/.libPaths?package=OmicNavigator&version=1.13.13" data-mini-rdoc="OmicNavigator::.libPaths">.libPaths</a></code>.</dd></dl>

Arguments

Get enrichments table from a study — getEnrichmentsTable

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


<dt>libraries</dt>
<dd>The directories to search for installed study packages. If
left as <code>NULL</code> (the default), then
<code><a href='https://rdrr.io/r/utils/installed.packages.html'>installed.packages</a></code> will use the result of
<code><a href='https://rdrr.io/r/base/libPaths.html'>.libPaths</a></code>.</dd>

</dl>

Get enrichments table from a study

getEnrichmentsTable: Get enrichments table from a study

Description

Usage

Value

Arguments