Convert Loom to SingleCellExperiment

Reads a Loom file through AnnData and creates a SingleCellExperiment while preserving supported count data, normalized data, metadata, feature metadata, and reductions.

Usage

convert_loom_to_sce(input, output)

Arguments

input

Path to an input .loom file.

output

Path to the output SingleCellExperiment .rds file.

Value

The output path, returned invisibly on success. If suitable raw count data cannot be identified, the function may return NULL invisibly without writing an output object.

Details

Raw counts are selected conservatively from an explicit counts layer when available or from X when it is non-negative and integer-like. The function does not guess raw counts from arbitrary named layers. Loom is a more limited interchange format than Seurat, SingleCellExperiment, or AnnData, so only components representable by the current mapping are preserved.