create_pseudobulk_mat.default: Create Pseudo-Bulk Matrix from scEpigenomics clusters &...

In vallotlab/IDclust: Iterative Differential Clustering for single-cell

Create Pseudo-Bulk Matrix from scEpigenomics clusters & replicates

Description

Create Pseudo-Bulk Matrix from scEpigenomics clusters & replicates

Usage

## Default S3 method:
create_pseudobulk_mat(
  object,
  by = "IDcluster",
  biological_replicate_col = NULL
)

Arguments

object	A SingleCellExperiment object containing scEpigenomics dataset with 'IDcluster' column.
by	A character specifying the name of the metadata column referencing the clusters.
biological_replicate_col	Optional. A column of the SingleCellExperiment object indicating the replicates or batches of the dataset in order to take in account biological/technical noise. If NULL, will create random layers of fake replicates.

Value

A pseudo-bulk matrix of cluster spread by replicates / batches / fake replicates.

Examples

if(requireNamespace("Seurat", quietly=TRUE)){
data("Seu", package = "IDclust")
mat <- create_pseudobulk_mat.default(object, by = "seurat_clusters")
}

vallotlab/IDclust documentation built on Feb. 16, 2023, 8:58 a.m.