mraplot

Plotting function for master regulator analysis performed by the _mra_ function

We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.

Federico M. Giorgi

corto

Inference of Gene Regulatory Networks

Daniele Mercatelli

Gonzalo Lopez-Garcia

mraplot function

<dl><dt>mraobj</dt>
<dd>The input object, output of the function mra</dd>
<dt>mrs</dt>
<dd>Either a numeric value indicating how many MRs to show, sorted by
significance, or a character vector specifying which TFs to show. Default is 5</dd>
<dt>title</dt>
<dd>Title of the plot (optional, default is "corto - Master Regulator Analysis")</dd>
<dt>pthr</dt>
<dd>The p-value at which the MR is considered significant. Default is 0.01</dd></dl>

Arguments

Plot a master regulator analysis — mraplot

<dl>

<dt>mraobj</dt>
<dd>The input object, output of the function mra</dd>


<dt>mrs</dt>
<dd>Either a numeric value indicating how many MRs to show, sorted by
significance, or a character vector specifying which TFs to show. Default is 5</dd>


<dt>title</dt>
<dd>Title of the plot (optional, default is "corto - Master Regulator Analysis")</dd>


<dt>pthr</dt>
<dd>The p-value at which the MR is considered significant. Default is 0.01</dd>

</dl>

mraplot: Plot a master regulator analysis

Description

Usage

Value

Arguments