Create a SCT Assay object — CreateSCTAssayObject • Seurat

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.

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

Details

Non-unique cell or feature names are not allowed. Please make unique before calling this function.