createIngresObjectFromSeurat

Create a new <code>ingres</code> object using the expression data in a
<code>Seurat</code> object.

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

ingres

Infer Gene Probabilistic Boolean Networks from Single-Cell Data

Francesca M. Buffa

createIngresObjectFromSeurat function

<dl><dt>seurat.object</dt>
<dd>A <code>Seurat</code> object with QC, scaling and
clustering already executed.</dd>
<dt>seurat.assay</dt>
<dd>The name of the assay to be imported,
normally 'RNA' or 'Spatial'.</dd>
<dt>slot</dt>
<dd>The name of the slot that contains the matrix to be used.</dd>
<dt>network.genes</dt>
<dd>A data frame with a column for node names
and another column for the corresponding entrez IDs.</dd>
<dt>network</dt>
<dd>A object of class <code>tbl_graph</code> representing
our network of interest.</dd></dl>

Arguments

Create a new ingres object using the expression data in a
Seurat object. — createIngresObjectFromSeurat

<dl>

<dt>seurat.object</dt>
<dd>A <code>Seurat</code> object with QC, scaling and
clustering already executed.</dd>


<dt>seurat.assay</dt>
<dd>The name of the assay to be imported,
normally 'RNA' or 'Spatial'.</dd>


<dt>slot</dt>
<dd>The name of the slot that contains the matrix to be used.</dd>


<dt>network.genes</dt>
<dd>A data frame with a column for node names
and another column for the corresponding entrez IDs.</dd>


<dt>network</dt>
<dd>A object of class <code>tbl_graph</code> representing
our network of interest.</dd>

</dl>

createIngresObjectFromSeurat: Create a new `ingres` object using the expression data in a `Seurat` object.

Description

Usage

Value

Arguments

Examples