Prepare Seurat objects for the SCExplorer

Prepares one or multiple Seurat objects for the SCExplorer app. It takes a Seurat object or a list of Seurat objects as input and outputs two hdf5 files: one for the data and one for the metadata.

Usage

PrepareSCExplorer(
  object,
  base_dir = "SCExplorer",
  data_file = "data.hdf5",
  meta_file = "meta.hdf5",
  assays = "RNA",
  layers = c("counts", "data"),
  ignore_nlevel = 100,
  write_tools = FALSE,
  write_misc = FALSE,
  compression_level = 6,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

object

A Seurat object or a list of Seurat objects.

base_dir

The base directory where the SCExplorer hdf5 files will be written.

data_file

Path to the output data file. If not provided, the file will be named "data.hdf5" in the current directory.

meta_file

Path to the output meta file. If not provided, the file will be named "meta.hdf5" in the current directory.

assays

The assays to include in the data file.

layers

The layers to include in the data file.

ignore_nlevel

The number of levels above which a metadata field will be ignored.

write_tools

Whether to write the tools information to the meta file.

write_misc

Whether to write the miscellaneous information to the meta file.

compression_level

Compression level for the HDF5 dataset.

overwrite

Whether to overwrite existing data in the data file.

verbose

Whether to print the message. Default is TRUE.

See also

CreateDataFile, CreateMetaFile, FetchH5, RunSCExplorer

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
PrepareSCExplorer(pancreas_sub, base_dir = "./SCExplorer")
} # }