asSingleCellExperiment: Transform to 'SingleCellExperiment'

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Transform to SingleCellExperiment

Description

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

Usage

asSingleCellExperiment(object)

Arguments

object	An object of class spata2.
...	The features to be renamed specified according to the following syntax: 'new_feature_name' = 'old_feature_name'. This applies to coordinates, too. E.g. ... ~ 'image_col' = 'x', 'image_row' = 'y' renames the coordinate variables to 'image_col' and 'image_row'.

Details

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

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

Value

An object of class SingleCellExperiment.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.