GRN-class: Create, represent, investigate, quantify and visualize...

In chrarnold/GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

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

Description

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_norm:

  • counts_orig:

  • consensusPeaks:

• RNA:

  • counts_norm.l:

  • counts_orig:

• metadata:

• TFs:

  • translationTable:

  • 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.

visualization

Stores visualization results, currently always empty. Feature in development.

isDev

Flag whether this is an object from the development version of the package

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 GRaNIE object

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

chrarnold/GRaNIE documentation built on April 28, 2022, 2:18 a.m.