get_sig_deggs

Get a table of all the significant interactions across categories

Performs multi-omic differential network
analysis by revealing differential interactions between molecular entities
(genes, proteins, transcription factors, or other biomolecules) across the
omic datasets provided.
For each omic dataset, a differential network is constructed where
links represent statistically significant differential interactions between
entities. These networks are then integrated into a comprehensive visualization
using distinct colors to distinguish interactions from different omic layers.
This unified display allows interactive exploration of cross-omic
patterns, such as differential interactions present at both transcript and
protein levels. For each link, users can access differential statistical
significance metrics (p values or adjusted p values, calculated via robust or
traditional linear regression with interaction term) and differential regression
plots.
The methods implemented in this package are described in Sciacca et al. (2023)
<doi:10.1093/bioinformatics/btad192>.

Elisabetta Sciacca

multiDEGGs

Multi-Omic Differentially Expressed Gene-Gene Pairs

Myles Lewis

get_sig_deggs function

<dl><dt>deggs_object</dt>
<dd>an object of class <code>deggs</code> generated by
<code>get_diffNetworks</code></dd>
<dt>assayDataName</dt>
<dd>name of the assayData of interest. If an unnamed list of
data was given to <code>get_diffNetworks</code>, <code>assayDataName</code> here will be the
number corresponding to the position of the data in the <code>assayDataList</code>
provided before (i.e. if transcriptomic data was second in the list, a list
of all its differential interactions can be obtained with assayDataName = 2,
if only one data table was provided assayDataName must be 1). Default 1.</dd>
<dt>sig_threshold</dt>
<dd>threshold for significance. Default 0.05.</dd></dl>

Arguments

Get a table of all the significant interactions across categories — get_sig_deggs

<dl>

<dt>deggs_object</dt>
<dd>an object of class <code>deggs</code> generated by
<code>get_diffNetworks</code></dd>


<dt>assayDataName</dt>
<dd>name of the assayData of interest. If an unnamed list of
data was given to <code>get_diffNetworks</code>, <code>assayDataName</code> here will be the
number corresponding to the position of the data in the <code>assayDataList</code>
provided before (i.e. if transcriptomic data was second in the list, a list
of all its differential interactions can be obtained with assayDataName = 2,
if only one data table was provided assayDataName must be 1). Default 1.</dd>


<dt>sig_threshold</dt>
<dd>threshold for significance. Default 0.05.</dd>

</dl>

get_sig_deggs: Get a table of all the significant interactions across categories

Description

Usage

Value

Arguments

Examples