initializeGRN: Initialize a 'GRN' object

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

Initialize a GRN object

Description

Initialize a GRN object

Usage

initializeGRN(objectMetadata = list(), outputFolder, genomeAssembly)

Arguments

objectMetadata	List. Default list(). Optional (named) list with an arbitrary number of elements, all of which capture metadata for the object. This is mainly used to distinguish GRN objects from one another by storing object-specific metadata along with the data.
outputFolder	Output folder, either absolute or relative to the current working directory. No default. Default output folder where all pipeline output will be put unless specified otherwise. We recommend specifying an absolute path. Note that for Windows-based systems, the path must be correctly specified with "/" as path separator.
genomeAssembly	Character. No default. The genome assembly of all data that to be used within this object. Currently, supported genomes are: hg19, hg38, and mm10.

Value

Empty GRN object

Examples

meta.l = list(name = "exampleName", date = "01.03.22")
GRN = initializeGRN(objectMetadata = meta.l, outputFolder = "output", genomeAssembly = "hg38")

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