Transform SPATA2 to Seurat

Transforms an SPATA2 object to an object of class Seurat. See details for more information.

asSeurat(
  object,
  process = TRUE,
  transfer_features = TRUE,
  assay_name = "Spatial",
  image_name = "slice1",
  verbose = NULL
)

Arguments

object

An object of class spata2.

process

Logical value. If TRUE, count matrix is processed. See details for more.

Use getInitiationInfo() to obtain argument input of your SPATA2 object initiation.

assay_name, image_name

Character values. Define the name with which to refer to the assay or the image in the Seurat object. Defaults to the default of the Seurat package.

verbose

Logical. If set to TRUE informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

Value

An object of class Seurat.

Details

If you have used initiateSpataObject_10X(), chances are that you have already specified input for various processing functions. asSeurat() creates a Seurat object from scratch. It has to, because even though many processing steps are run with the Seurat object as background SPATA2 does not net all its content and to keep SPATA2 objects as small as possible not everything is transferred from the Seurat object.

If process = TRUE, the input you've given to initiateSpataObject_10X() is taken to conduct the same processing. To check what you have defined as input, you can use the function getInititationInfo().