addEnrichments

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. 

addEnrichments function

<dl><dt>study</dt>
<dd>An OmicNavigator study created with <code>createStudy</code></dd>
<dt>enrichments</dt>
<dd>The enrichment results from each model. The input is a
nested named list. The names of the list correspond to the model names.
Each list element should be a list of the annotation databases tested
(<code>addAnnotations</code>). The names of the list correspond to the
annotation databases. Each list element should be another list of tests
(<code>addTests</code>). The names correspond to the tests performed. Each
of these elements should be a data frame with enrichment results. Each
table must contain the following columns: "termID", "description",
"nominal" (the nominal statistics), and "adjusted" (the statistics after
adjusting for multiple testing). Any additional columns are ignored.</dd>
<dt>reset</dt>
<dd>Reset the data prior to adding the new data (default:
<code>FALSE</code>). The default is to add to or modify any previously added data
(if it exists). Setting <code>reset = TRUE</code> enables you to remove existing
data you no longer want to include in the study.</dd></dl>

Arguments

Add enrichment results — addEnrichments

<dl>

<dt>study</dt>
<dd>An OmicNavigator study created with <code>createStudy</code></dd>


<dt>enrichments</dt>
<dd>The enrichment results from each model. The input is a
nested named list. The names of the list correspond to the model names.
Each list element should be a list of the annotation databases tested
(<code>addAnnotations</code>). The names of the list correspond to the
annotation databases. Each list element should be another list of tests
(<code>addTests</code>). The names correspond to the tests performed. Each
of these elements should be a data frame with enrichment results. Each
table must contain the following columns: "termID", "description",
"nominal" (the nominal statistics), and "adjusted" (the statistics after
adjusting for multiple testing). Any additional columns are ignored.</dd>


<dt>reset</dt>
<dd>Reset the data prior to adding the new data (default:
<code>FALSE</code>). The default is to add to or modify any previously added data
(if it exists). Setting <code>reset = TRUE</code> enables you to remove existing
data you no longer want to include in the study.</dd>

</dl>

Add enrichment results

addEnrichments: Add enrichment results

Description

Usage

Value

Arguments