asGiotto: Transform 'spata2' object to 'Giotto'

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

Transform spata2 object to Giotto

Description

Transforms an spata2 object object to an object of class Giotto. See details for more information.

Usage

asGiotto(object, transfer_features = TRUE, verbose = NULL)

Arguments

object	An object of either one of the following classes: Seurat, SingleCellExperiment, AnnDataR6
transfer_features, transfer_meta_data	Logical or character. Specifies if meta/feature, e.g clustering, data from the input object is transferred to the output object. If TRUE, all variables of the feature/meta data.frame are transferred. If character, named variables are transferred. If FALSE, none are transferred.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Details

The object is created using the count matrix of the input as well as coordinates. If an image is found it is transferred, too. No further processing is done (e.g. Giotto::normalizeGiotto(), Giotto::runPCA()).

Value

An object of class Giotto.

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