Obtain processed data matrix

Extracts a processed data matrix.

getProcessedMatrix(object, ...)

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

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

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.

mtr_name

Character value. The name of the processed matrix of interest.

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 numeric matrix with rownames corresponding to molecule names and column names corresponding to barcodes.

Note

The argument mtr_name must be specified in contrast to getMatrix().

See also

getCountMatrix(), getMatrix(), [getProcessedMatrixNames()'], [getMatrixNames()`]