Save corresponding objects

Family of functions to save corresponding objects of different analysis platforms. See details and value for more information.

saveCorrespondingCDS(
  cds,
  object,
  directory_cds = NULL,
  combine_with_wd = FALSE,
  verbose = NULL
)

saveCorrespondingSeuratObject(
  seurat_object,
  object,
  directory_seurat = NULL,
  combine_with_wd = FALSE,
  verbose = NULL
)

saveSpataObject(object, directory_spata = NULL, verbose = NULL, ...)

Arguments

cds

A valid cell-data-set. (from the monocle3 platform)

object

A valid spata-object.

combine_with_wd

Character value or FALSE. If specified with a character value (default: '/') the input of new_directory is considered to be a relative directory and is combined with the current working directory (base::getwd()) separated with the character string specified. If set to FALSE the input of new_directory is taken as is.

seurat_object

A valid seurat-object. (from the Seurat platform)

directory_spata, directory_cds_directory_seurat_object

Character value or NULL. Set details for more.

...

Named arguments whoose default input you want to override.

Value

Apart from their side effect (saving the object of interest) all three functions return the provided, updated spata-object.

Details

If directory_<platform> is set to NULL (the default) all functions first check if the spata-object contains any deposited default directories. If so the specified object to be saved is saved under that direction. If directory_<platform> is specified as a character it's input is taken as the directory under which to store the object and the deposited directory is overwritten such that the next time you load the spata-object it contains the updated directory. In order for that to work the saveCorresponding*()-functions - apart from saving the object of interest - return the updated spata-object while saveSpataObject() simply returns an invisible TRUE as the new directory (if provided) is stored inside the object before it is saved.