getCountMatrix: Obtain raw counts

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain raw counts

Description

Extracts the unprocessed raw count matrix.

Usage

getCountMatrix(object, ...)

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

## S4 method for signature '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.

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