Create_CellBender_Merged_Seurat: Create Seurat Object with Cell Bender and Raw data

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

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,
  ...
)

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.

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).

Examples

## Not run: 
seurat_obj <- Create_CellBender_Merged_Seurat(raw_cell_bender_matrix = cb_matrix,
raw_counts_matrix = cr_matrix)

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.