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.