scCustomize (version 3.0.1)

Create_CellBender_Merged_Seurat: Create Seurat Object with Cell Bender and Raw data

Description

Enables easy creation of Seurat object which contains both cell bender data and raw count data as separate assays within the object.

Usage

Create_CellBender_Merged_Seurat(
  raw_cell_bender_matrix = NULL,
  raw_counts_matrix = NULL,
  raw_assay_name = "RAW",
  min_cells = 5,
  min_features = 200,
  ...
)

Value

A Seurat Object contain both the Cell Bender corrected counts ("RNA" assay) and uncorrected counts ("RAW" assay; or other name specified to raw_assay_name).

Arguments

raw_cell_bender_matrix

matrix file containing the cell bender correct counts.

raw_counts_matrix

matrix file contain the uncorrected Cell Ranger (or other) counts.

raw_assay_name

a key value to use specifying the name of assay. Default is "RAW".

min_cells

value to supply to min.cells parameter of CreateSeuratObject. Default is 5.

min_features

value to supply to min.features parameter of CreateSeuratObject. Default is 200.

...

Extra parameters passed to CreateSeuratObject.

Examples

if (FALSE) {
seurat_obj <- Create_CellBender_Merged_Seurat(raw_cell_bender_matrix = cb_matrix,
raw_counts_matrix = cr_matrix)
}