ingres-class

ingres

ingresClass

ingresObject

Given a gene regulatory boolean network and a RNA-seq dataset,
this package computes protein activity normalised enrichment scores
using 'VIPER', and then produces a probabilistic network using the scores
as probabilities for fixed node activation or deactivation,
in addition to the original Boolean functions.
For more information, refer to the preprint:
Victori and Buffa (2022) <doi:10.1101/2022.09.04.506528>.

Pedro Victori

Infer Gene Probabilistic Boolean Networks from Single-Cell Data

Francesca M. Buffa

ingres-class function

<dl>
<dt><code>expression</code></dt>
<dd>matrix.</dd></dl>
<dt><code>idents</code></dt>
<dd>data.frame.</dd>
<dt><code>network.genes</code></dt>
<dd>data.frame.</dd>
<dt><code>viper</code></dt>
<dd>data.frame.</dd>
<dt><code>cluster.pbn</code></dt>
<dd>data.frame.</dd>
<dt><code>single.cell.pbn</code></dt>
<dd>data.frame.</dd>
<dt><code>network</code></dt>
<dd><code>tbl_graph</code>.</dd>

Slots

The ingres class. — ingres-class

<dl>
<dt><code>expression</code></dt>
<dd>matrix.</dd>


<dt><code>idents</code></dt>
<dd>data.frame.</dd>


<dt><code>network.genes</code></dt>
<dd>data.frame.</dd>


<dt><code>viper</code></dt>
<dd>data.frame.</dd>


<dt><code>cluster.pbn</code></dt>
<dd>data.frame.</dd>


<dt><code>single.cell.pbn</code></dt>
<dd>data.frame.</dd>


<dt><code>network</code></dt>
<dd><code>tbl_graph</code>.</dd>


</dl>

ingres-class: The ingres class.

Description

Arguments

Value

Slots