getProcessedMatrix: Obtain processed data matrix

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain processed data matrix

Description

Extracts a processed data matrix.

Usage

getProcessedMatrix(object, ...)

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

## S4 method for signature '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()']

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.