save_monocle_objects: Save a Monocle3 full cell_data_set.

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Save a Monocle3 full cell_data_set.

Description

Save a Monocle3 full cell_data_set to a specified directory by writing the R objects to RDS files and the nearest neighbor indexes to index files. The assays objects are saved as HDF5Array files when hdf5_assays=TRUE or when the cell_data_set assays are HDF5Array objects. If any assay in the cell_data set is an HDF5 object, all assays must be. When save_monocle_objects is run with hdf5_assays=TRUE, the load_monocle_objects function loads the saved assays into HDF5Array objects in the resulting cell_data_set. Note: operations such as preprocess_cds that are run on assays stored as HDF5Arrays are much, much slower than the same operations run on assays stored as in-memory matrices. You may want to investigate parameters related to the Bioconductor DelayedArray and BiocParallel packages in this case.

Usage

save_monocle_objects(
  cds,
  directory_path,
  hdf5_assays = FALSE,
  comment = "",
  verbose = TRUE
)

Arguments

cds	a cell_data_set to save.
directory_path	a string giving the name of the directory in which to write the object files.
hdf5_assays	a boolean determining whether the non-HDF5Array assay objects are saved as HDF5 files. At this time cell_data_set HDF5Array assay objects are stored as HDF5Assay files regardless of the hdf5_assays parameter value.
comment	a string with optional notes that is saved with the objects.
verbose	a boolean determining whether to print information about the saved files.

Value

none.

Examples

  ## Not run: 
    cds <- load_a549()
    save_monocle_objects(cds, 'mo')
  
## End(Not run)

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.