fcor

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

fcor function

<dl><dt>inmat</dt>
<dd>An input matrix with features as rows and samples as columns</dd>
<dt>centroids</dt>
<dd>A character vector indicating the centroids</dd>
<dt>r</dt>
<dd>A numeric correlation threshold</dd></dl>

Arguments

A fast correlation function — fcor

<dl>

<dt>inmat</dt>
<dd>An input matrix with features as rows and samples as columns</dd>


<dt>centroids</dt>
<dd>A character vector indicating the centroids</dd>


<dt>r</dt>
<dd>A numeric correlation threshold</dd>

</dl>

fcor: A fast correlation function

Description

Usage

Value

Arguments