Convert H5MU files to H5AD files (extract single modality)

Converts via streaming: h5mu -> h5seurat (temp) -> h5ad. Only the first modality (or assay) is exported to h5ad.

Usage

H5MUToH5AD(
  source,
  dest,
  assay = NULL,
  overwrite = FALSE,
  gzip = 4L,
  verbose = TRUE,
  stream = TRUE
)

H5MUToH5AD(
  source,
  dest,
  assay = NULL,
  overwrite = FALSE,
  gzip = 4L,
  verbose = TRUE,
  stream = TRUE
)

Arguments

source

Path to input .h5mu file

dest

Path for output .h5ad file

assay

Assay name to export (default: first modality)

overwrite

If TRUE, overwrite existing output

gzip

Gzip compression level (0-9)

verbose

Show progress messages

stream

If TRUE (default), use streaming. If FALSE, load into R.

modality

Name of modality to extract from h5mu file

Value

Returns a handle to dest as an H5File object

Invisibly returns dest