Subset a SingleCellExperiment by Cell Type
subsetSCE.RdThis function facilitates the subsetting of a SingleCellExperiment object to a specified number of cells,
with an option to maintain an even or proportional distribution across different cell types. It offers flexibility
in handling scenarios where insufficient cells of a specific type are available and ensures reproducibility through
the option to set a seed for random sampling.
Usage
subsetSCE(
sce,
cell_type_col = "celltype_major",
scenario = "even",
ncells = 1000,
notEnough = "asis",
seed = 12345
)Arguments
- sce
A
SingleCellExperimentobject containing cell type annotations. The function applies subsetting operations on this object to achieve a targeted composition of cell types.- cell_type_col
A character string indicating the column name within
colDataof theSingleCellExperimentobject that contains cell type information. This column is used to identify and categorize cells by type for subsetting.- scenario
Specifies the strategy for cell selection across types:
"even"for equal numbers from each cell type, or"mirror"to reflect the proportional representation of cell types in the subset as in the original dataset.- ncells
The target total number of cells for the subsetted object. Defaults to 1000. This parameter dictates the overall size of the subsetted
SingleCellExperiment.- notEnough
Defines the behavior when there are not enough cells of a certain type to meet the subsetting criteria:
"remove"to exclude that cell type entirely, or"asis"to include all available cells of that type despite falling short of the target number.- seed
An optional numeric value to set the random seed for reproducibility of the subsetting process. This ensures that the subset selection can be replicated in future analyses.