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Write a Seurat object to h5mu format

Source: R/Convert.R
writeH5MU.Rd

Writes a multi-assay Seurat object to an h5mu file, with each assay becoming a separate modality under /mod/{modality}/. Works with Seurat V5 Assay5 objects. No external dependencies required.

Usage

writeH5MU(
  object,
  filename = NULL,
  assays = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

object

A Seurat object with one or more assays

filename

Output h5mu file path. If NULL, derived from project name.

assays

Character vector of assay names to export (default: all)

overwrite

Overwrite existing file (default: FALSE)

verbose

Print progress messages (default: TRUE)

Value

Invisibly returns the output filename

Details

The h5mu format is designed for multimodal data and stores each Seurat assay as a separate modality under /mod/{modality_name}. This function:

  • Extracts each specified assay from the Seurat object

  • Converts assays to modality structure

  • Writes counts and data layers for each modality

  • Preserves cell metadata in global /obs and per-modality obs

  • Maintains dimensional reductions and graphs

Assay Mapping

By default, Seurat assay names are mapped to standard MuData modality names:

  • RNA -> rna

  • ADT -> prot

  • ATAC -> atac

  • Spatial -> spatial

  • Other names are converted to lowercase

See also

readH5MU, scConvert, as.h5mu

Examples

if (FALSE) { # \dontrun{
# Write a multi-assay Seurat object (e.g. CITE-seq with RNA + ADT)
writeH5MU(seurat_obj, filename = "multimodal.h5mu")

# Write specific assays only
writeH5MU(seurat_obj, filename = "rna_only.h5mu", assays = "RNA")
} # }