This function 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",
DataFile = "Data.hdf5",
MetaFile = "Meta.hdf5",
assays = "RNA",
slots = c("counts", "data"),
ignore_nlevel = 100,
write_tools = FALSE,
write_misc = FALSE,
compression_level = 6,
overwrite = FALSE
)Arguments
- object
A Seurat object or a list of Seurat objects.
- base_dir
The base directory where the SCExplorer hdf5 files will be written. Default is "SCExplorer".
- DataFile
Path to the output data file. If not provided, the file will be named "Data.hdf5" in the current directory.
- MetaFile
Path to the output meta file. If not provided, the file will be named "Meta.hdf5" in the current directory.
- assays
Character vector specifying the assays to include in the data file. Default is "RNA".
- slots
Character vector specifying the slots to include in the data file. Default is "data".
- ignore_nlevel
The number of levels above which a metadata field will be ignored. Default is 100.
- write_tools
A logical value indicating whether to write the tools information to the meta file. Default is FALSE.
- write_misc
A logical value indicating whether to write the miscellaneous information to the meta file. Default is FALSE.
- compression_level
Compression level for the HDF5 dataset. Default is 6.
- overwrite
Logical value indicating whether to overwrite existing data in the data file. Default is FALSE.
Examples
if (FALSE) { # \dontrun{
data("pancreas_sub")
pancreas_sub <- Standard_SCP(pancreas_sub)
PrepareSCExplorer(pancreas_sub, base_dir = "./SCExplorer")
} # }