create_pseudobulk_mat.Seurat: Create Pseudo-Bulk Matrice from scRNA clusters & replicates

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

Create Pseudo-Bulk Matrice from scRNA clusters & replicates

Description

Create Pseudo-Bulk Matrice from scRNA clusters & replicates

Usage

## S3 method for class 'Seurat'
create_pseudobulk_mat(
  object,
  by = "IDcluster",
  biological_replicate_col = NULL,
  assay = "RNA"
)

Arguments

by	A character specifying the name of the metadata column referencing the clusters.
biological_replicate_col	Optional. A column of the Seurat 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.
assay	Assay to use.
Seu	A Seurat object containing scRNA dataset with 'IDcluster' column.

Value

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

Examples

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

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