convert_anndata_to_sce: Convert AnnData to SingleCellExperiment

In scFlex: Flexible Conversion Between Single-Cell Data Objects

Convert AnnData to SingleCellExperiment

Description

Converts an AnnData H5AD file to a SingleCellExperiment object while preserving counts, normalized expression when available, cell metadata, feature metadata, and dimensional reductions.

Usage

convert_anndata_to_sce(input, output)

Arguments

input	Path to an AnnData H5AD file.
output	Path where the converted SingleCellExperiment RDS file should be written.

Details

An explicit layers["counts"] matrix is preferred as the counts assay. Fractional values are accepted in an explicit counts layer as long as all values are finite and non-negative. If no explicit counts layer is present, X is used as counts only when its values are finite, non-negative, and integer-like.

Normalized expression is optional. If layers["logcounts"] is present it is stored as the SCE logcounts assay. Otherwise, X is used as logcounts when it was not already used as the counts matrix.

Value

Invisibly returns the output file path.

scFlex documentation built on Sept. 29, 2026, 5:10 p.m.