saveRDS: Save 'SpatialExperiment' objects as RDS files

In SpatialDDLS: Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

Save SpatialExperiment objects as RDS files

Description

Save SpatialExperiment and DeconvDLModel objects as RDS files. keras models cannot be stored natively as R objects (e.g. RData or RDS files). By saving the architecture as a JSON-like character object and the weights as a list, it is possible to retrieve a functional model and make new predictions. If the trained.model slot is empty, the function will behave as usual. Note: with this option, the state of optimizer is not saved, only model's architecture and weights. It is possible to save the entire model as an HDF5 file with the saveTrainedModelAsH5 function and load it into a SpatialExperiment object with the loadTrainedModelFromH5 function. See documentation for details.

Usage

saveRDS(
  object,
  file,
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S4 method for signature 'DeconvDLModel'
saveRDS(
  object,
  file,
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S4 method for signature 'SpatialDDLS'
saveRDS(
  object,
  file,
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

Arguments

object	SpatialExperiment or DeconvDLModel object to be saved
file	File path where the object will be saved
ascii	a logical. If TRUE or NA, an ASCII representation is written; otherwise (default), a binary one is used. See the comments in the help for save.
version	the workspace format version to use. NULL specifies the current default version (3). The only other supported value is 2, the default from R 1.4.0 to R 3.5.0.
compress	a logical specifying whether saving to a named file is to use "gzip" compression, or one of "gzip", "bzip2" or "xz" to indicate the type of compression to be used. Ignored if file is a connection.
refhook	a hook function for handling reference objects.

Value

No return value, saves a SpatialExperiment object as an RDS file on disk.

See Also

SpatialExperiment saveTrainedModelAsH5

SpatialDDLS documentation built on Oct. 31, 2024, 5:07 p.m.