Obtain raw counts — getCountMatrix • SPATA2

Extracts the unprocessed raw count matrix.

getCountMatrix(object, ...)

# S4 method for class 'SPATA2'
getCountMatrix(object, assay_name = activeAssay(object), ...)

# S4 method for class 'MolecularAssay'
getCountMatrix(object, ...)

Arguments

object: An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...: Used to absorb deprecated arguments or functions.
assay_name: Only relevant if the SPATA2 object contains more than one assay: Denotes the assay of interest and thus the molecular modality to use. Defaults to the active assay as set by activateAssay().

Value

A matrix of unprocessed molecular counts with rownames corresponding to the features and column names corresponding to the barcodes.