addAssays

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. 

addAssays function

<dl><dt>study</dt>
<dd>An OmicNavigator study created with <code>createStudy</code></dd>
<dt>assays</dt>
<dd>The assays from the study. The input object is a list of data
frames (one per model). The row names should correspond to the featureIDs
(<code>addFeatures</code>). The column names should correspond to the
sampleIDs (<code>addSamples</code>). The data frame should only contain
numeric values. To share a data frame across multiple models, use the
modelID "default".</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 assays — addAssays

<dl>

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


<dt>assays</dt>
<dd>The assays from the study. The input object is a list of data
frames (one per model). The row names should correspond to the featureIDs
(<code>addFeatures</code>). The column names should correspond to the
sampleIDs (<code>addSamples</code>). The data frame should only contain
numeric values. To share a data frame across multiple models, use the
modelID "default".</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 assays

addAssays: Add assays

Description

Usage

Value

Arguments