createNetworkGenesTemplate

Create a network genes data frame. Optionally store it as csv
and open it for editing
To create an ingres object, a data frame with the network nodes and
the corresponding gene symbols must be provided. This function simplifies
the process. If the gene nodes are correct gene symbols, then modification
is not needed and the returned data frame can be directly passed to
the ingres constructors.

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

createNetworkGenesTemplate function

<dl><dt>network</dt>
<dd>A tidygraph network.</dd>
<dt>dir</dt>
<dd>The directory where the csv will be stored, if applicable.</dd>
<dt>store</dt>
<dd>If true, store the data frame as a csv</dd>
<dt>modify</dt>
<dd>If true, and store is also true,
open it to be modified by the user</dd></dl>

Arguments

Create a network genes data frame. Optionally store it as csv
and open it for editing
To create an ingres object, a data frame with the network nodes and
the corresponding gene symbols must be provided. This function simplifies
the process. If the gene nodes are correct gene symbols, then modification
is not needed and the returned data frame can be directly passed to
the ingres constructors. — createNetworkGenesTemplate

<dl>

<dt>network</dt>
<dd>A tidygraph network.</dd>


<dt>dir</dt>
<dd>The directory where the csv will be stored, if applicable.</dd>


<dt>store</dt>
<dd>If true, store the data frame as a csv</dd>


<dt>modify</dt>
<dd>If true, and store is also true,
open it to be modified by the user</dd>

</dl>

Create a network genes data frame. Optionally store it as csv
and open it for editing
To create an ingres object, a data frame with the network nodes and
the corresponding gene symbols must be provided. This function simplifies
the process. If the gene nodes are correct gene symbols, then modification
is not needed and the returned data frame can be directly passed to
the ingres constructors.

Description

Usage

Value

Arguments

Examples