CreateSCTAssayObject: Create a SCT Assay object

In satijalab/seurat: Tools for Single Cell Genomics

Create a SCT Assay object

Description

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

Details

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

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.