Obtain a data matrix

Extracts a matrix or multiple matrices of molecular data.

getMatrix(object, mtr_name = NULL, ...)

# S4 method for class 'SPATA2'
getMatrix(object, mtr_name = NULL, assay_name = activeAssay(object))

# S4 method for class 'MolecularAssay'
getMatrix(object, mtr_name = NULL)

getMatrices(object, ...)

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

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

Arguments

object

An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.

mtr_name

Character value. The name of the matrix to extract. If NULL, defaults to the active matrix of the provided or specified assay.

...

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 numeric matrix with rownames corresponding to molecule names and column names corresponding to barcodes. Or a named list of such in case of getMatrices().

See also

getCountMatrix() to extract raw counts without additional argument specification required, getMatrixNames() for a vector of all matrix names of an assay, getProcessedMatrixNames() for a vector of all processed matrix of an assay.