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 indexes 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 indexes when the preprocess_cds and reduce_dimension functions are run with the make_nn_index=TRUE parameter. These indexes 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 directory_path.

Usage

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

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.

Value

none.

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 April 7, 2024, 9:24 p.m.