initiate_grn: Initiate the 'RegulatoryNetwork' object.

In quadbiolab/Pando: Inferring regulomes from multi-modal single-cell genomics data

Initiate the RegulatoryNetwork object.

Description

Initiate the RegulatoryNetwork object.

Initiate the RegulatoryNetwork object.

Usage

initiate_grn(object, ...)

## S3 method for class 'Seurat'
initiate_grn(
  object,
  regions = NULL,
  peak_assay = "peaks",
  rna_assay = "RNA",
  exclude_exons = TRUE
)

## S3 method for class 'GRNData'
initiate_grn(
  object,
  regions = NULL,
  peak_assay = "peaks",
  rna_assay = "RNA",
  exclude_exons = TRUE
)

Arguments

object	An object.
regions	Candidate regions to consider for binding site inference. If NULL, all peaks regions are considered.
peak_assay	A character vector indicating the name of the chromatin accessibility assay in the Seurat object.
rna_assay	A character vector indicating the name of the gene expression assay in the Seurat object.
exclude_exons	Logical. Whether to consider exons for binding site inference.

Value

A GRNData object containing a RegulatoryNetwork object.

quadbiolab/Pando documentation built on April 22, 2024, 8:14 a.m.