Direct Seurat-to-h5ad write (single-pass, no intermediate h5Seurat)

Writes a Seurat object directly to an h5ad file, bypassing the two-pass Seurat -> h5Seurat -> h5ad pipeline. This avoids 3x I/O overhead and provides significant speedup for in-memory Seurat objects.

Usage

DirectSeuratToH5AD(
  object,
  filename,
  assay = DefaultAssay(object = object),
  overwrite = FALSE,
  verbose = TRUE,
  standardize = FALSE
)

Arguments

object

A Seurat object

filename

Output h5ad file path

assay

Name of the assay to write (default: DefaultAssay)

overwrite

Overwrite existing file (default: FALSE)

verbose

Print progress messages (default: TRUE)

standardize

Convert Seurat metadata names to scanpy conventions

Value

Invisibly returns the output filename