getGRNConnections: Extract connections from a 'GRN' object

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

Extract connections from a GRN object

Description

Extract connections from a GRN object

Usage

getGRNConnections(
  GRN,
  type = "all.filtered",
  permuted = FALSE,
  include_TF_gene_correlations = FALSE
)

Arguments

GRN	Object of class GRN
type	Character. Default all.filtered. Must be one of TF_peaks, peak_genes, all.filtered. The type of connections to retrieve.
permuted	TRUE or FALSE. Default FALSE. Should the permuted data be taken (TRUE) or the non-permuted, original one (FALSE)?
include_TF_gene_correlations	Logical. TRUE or FALSE. Should TFs and gene correlations be returned as well? If set to TRUE, they must have been computed beforehand with add_TF_gene_correlation.

Value

A data frame with the connections. Importantly, this function does **NOT** return a GRN object.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
GRN_con.all.df = getGRNConnections(GRN)

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