Create Seurat Object with Cell Bender and Raw data

Source: R/Read_&_Write_Data.R

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

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

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