asSingleCellExperiment: Transform SPATA2 object to SingleCellExperiment object

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Transform SPATA2 object to SingleCellExperiment object

Description

Transforms an SPATA2 object to an object of class SingleCellExperiment. See details for more information.

Usage

asSingleCellExperiment(
  object,
  assay_name = activeAssay(object),
  bayes_space = FALSE,
  verbose = NULL
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
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().
bayes_space	Logical. If TRUE, the function creates an object fitted to the requirements for the BayesSpace pipeline.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Details

Output object contains the count matrix in slot @assays and feature data.frame combined with coordinates in slot @colData.

Slot @metadata is a list that contains the image object.

Value

An object of class SingleCellExperiment.

Examples

library(SPATA2)
library(SingleCellExperiment)

data("example_data")

object <- example_data$object_UKF275T_diet

sce <- asSingleCellExperiment(object)

class(sce)

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