build_eGRN_graph: Builds a graph out of a set of connections

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

Builds a graph out of a set of connections

Description

Builds a graph out of a set of connections

Usage

build_eGRN_graph(
  GRN,
  model_TF_gene_nodes_separately = FALSE,
  allowLoops = FALSE,
  removeMultiple = FALSE,
  directed = FALSE,
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
model_TF_gene_nodes_separately	TRUE or FALSE. Default FALSE. Should TF and gene nodes be modeled separately? If set to TRUE,this may lead to unwanted effects in case of TF-TF connections (i.e., a TF regulating another TF)
allowLoops	TRUE or FALSE. Default FALSE. Allow loops in the network (i.e., a TF that regulates itself)
removeMultiple	TRUE or FALSE. Default FALSE. Remove loops with the same start and end point? This can happen if multiple TF originate from the same gene, for example.
directed	TRUE or FALSE. Default FALSE. Should the network be directed?
forceRerun	TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.

Value

The same GRN object.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
GRN = build_eGRN_graph(GRN, forceRerun = FALSE)

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