Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (eGRNs)

The class GRN stores data and information related to our eGRN approach to construct enhancer-mediated gene regulatory networks out of open chromatin and RNA-Seq data. See the description below for more details, and visit our project website at https://grp-zaugg.embl-community.io/GRaNIE and have a look at the various Vignettes.

Slots

data

Currently stores 4 different types of data:

• peaks:

  • counts:

  • counts_metadata:

• RNA:

  • counts:

  • counts_metadata:

  • counts_permuted_index:

• TFs:

  • TF_activity:

  • TF_peak_overlap:

  • classification:

config

Contains general configuration data and parameters such as parameters, files, directories, flags, and recorded function parameters.

connections

Stores various types of connections

annotation

Stores annotation data for peaks and genes

stats

Stores statistical and summary information for a GRN network. Currently, connection details are stored here.

graph

Stores the eGRN graph related information and data structures

Constructors

Currently, a GRN object is created by executing the function initializeGRN.

Accessors

In the following code snippets, GRN is a GRN object.

# Get general annotation of a GRN object from the GRaNIE package

nPeaks(GRN)), nTFs(GRN)) and nGenes(GRN)): Retrieve the number of peaks, TFs and genes, respectively, that have been added to the object (both before and after filtering)