save_transform_models: Save cell_data_set transform models.

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

Save cell_data_set transform models.

Description

Save the transform models in the cell_data_set to the specified directory by writing the R objects to RDS files and the nearest neighbor indices to index files. save_transform_models saves transform models made by running the preprocess_cds and reduce_dimension functions on an initial cell_data_set. Subsequent cell_data_sets are transformed into the reduced dimension space of the initial cell_data_set by loading the new data into a new cell_data_set, loading the initial data set transform models into the new cell_data_set using the load_transform_models function, and applying those transform models to the new data set using the preprocess_transform() and reduce_dimension_transform() functions. In this case, do not run the preprocess_cds() or reduce_dimension() functions on the new cell_data_set. Additionally, save_transform_models() saves nearest neighbor indices when the preprocess_cds() and reduce_dimension() functions are run with the make_nn_index=TRUE parameter. These indices are used to find matches between cells in the new processed cell_data_set and the initial cell_data_set using index search functions. For more information see the help for transfer_cell_labels(). save_transform_models() saves the models to a directory given by the directory_path parameter.

Usage

save_transform_models(
  cds,
  directory_path,
  comment = "",
  verbose = TRUE,
  archive_control = list()
)

Arguments

cds	a cell_data_set with existing models.
directory_path	a string giving the name of the directory in which to write the model files.
comment	a string with optional notes that is saved with the objects.
verbose	a boolean determining whether to print information about the saved files.
archive_control	a list that is used to control archiving the output directory. The archive_control parameters are archive_type a string giving the method used to archive the directory. The acceptable values are "tar" and "none". The directory is not archived when archive_type is "none". The default is "tar". archive_compression a string giving the type of compression applied to the archive file. The acceptable values are "none", "gzip", "bzip2", and "xz". The default is "none".

Value

none.

Notes

• The R tar archive function used by Monocle3 may have a limited output file size of 8 GB. If you encounter this problem, you can set the environment variable "tar" to a tar executable that has no size limit, for example, gnu tar. You can do this in the $HOME/.monoclerc file by adding a line consisting of Sys.setenv('tar' = paste(Sys.getenv("TAR"), "-H", "gnu")). See the R 'tar' documentation for more information.

Examples

  ## Not run: 
    cds <- load_a549()
    cds <- preprocess_cds(cds)
    cds <- reduce_dimension(cds)
    save_transform_models(cds, 'tm')
  
## End(Not run)

cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.