Create Seurat Object with Cell Bender and Raw data
Source:R/Read_&_Write_Data.R
Create_CellBender_Merged_Seurat.RdEnables 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 = deprecated(),
min_features = deprecated(),
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
![[Deprecated]](figures/lifecycle-deprecated.svg)
soft-deprecated. See min.cells.- min_features
- soft-deprecated. See
min.features. - 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)
}