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Convert SingleCellExperiment to AnnData

Source: R/convert_to_anndata.R
convert_to_anndata.Rd

This function converts a SingleCellExperiment (SCE) object to an AnnData object. It processes assays, dimensional reductions, and metadata, including alternative experiments (altExps). The main assay is used as the primary data matrix in the AnnData object.

Usage

convert_to_anndata(sce, assayName = "counts", useAltExp = TRUE)

Arguments

sce

A SingleCellExperiment object to be converted.

assayName

The name of the assay to use as the main data matrix in AnnData. Defaults to "counts".

useAltExp

Logical indicating whether to process and include alternative experiments (altExps). Defaults to TRUE.

Value

An AnnData object containing the data from the SingleCellExperiment object.

Details

The function first prints a summary of the input SingleCellExperiment object and checks for alternative experiments (altExps). If altExps are found, they are processed recursively and stored in the `uns` slot of the AnnData object, unless the `useAltExp` parameter is set to FALSE. The specified assay is used as the primary data matrix (anndata.X), and all other assays are stored in the `layers` slot. Dimensional reductions are stored in the `obsm` slot, and metadata is organized into `obs`, `var`, `obsp`, `varp`, and `uns` slots as appropriate. The function includes detailed error handling to ensure that all data is correctly transferred to the AnnData object.

Examples

if (FALSE) { # \dontrun{
library(SingleCellExperiment)
library(anndata)
sce <- SingleCellExperiment::SingleCellExperiment(list(counts = matrix(1:4, ncol = 2)))
ad <- convert_to_anndata(sce)
} # }