Create a SCT object from a feature (e.g. gene) expression matrix and a list of SCTModels. The expected format of the input matrix is features x cells.
Usage
CreateSCTAssayObject(
counts,
data,
scale.data = NULL,
umi.assay = "RNA",
min.cells = 0,
min.features = 0,
SCTModel.list = NULL
)Arguments
- counts
Unnormalized data such as raw counts or TPMs
- data
Prenormalized data; if provided, do not pass
counts- scale.data
a residual matrix
- umi.assay
The UMI assay name. Default is RNA
- min.cells
Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff
- min.features
Include cells where at least this many features are detected
- SCTModel.list
list of SCTModels