Convert simulation output to different formats.

For use with other packages compatible with dyno, anndata, SingleCellExperiment, or Seurat.

as_dyno(
  model,
  store_dimred = !is.null(model$simulations$dimred),
  store_cellwise_grn = !is.null(model$experiment$cellwise_grn),
  store_rna_velocity = !is.null(model$experiment$rna_velocity)
)

as_anndata(
  model,
  store_dimred = !is.null(model$simulations$dimred),
  store_cellwise_grn = !is.null(model$experiment$cellwise_grn),
  store_rna_velocity = !is.null(model$experiment$rna_velocity)
)

as_sce(
  model,
  store_dimred = !is.null(model$simulations$dimred),
  store_cellwise_grn = !is.null(model$experiment$cellwise_grn),
  store_rna_velocity = !is.null(model$experiment$rna_velocity)
)

as_seurat(
  model,
  store_dimred = !is.null(model$simulations$dimred),
  store_cellwise_grn = !is.null(model$experiment$cellwise_grn),
  store_rna_velocity = !is.null(model$experiment$rna_velocity)
)

as_list(
  model,
  store_dimred = !is.null(model$simulations$dimred),
  store_cellwise_grn = !is.null(model$experiment$cellwise_grn),
  store_rna_velocity = !is.null(model$experiment$rna_velocity)
)

wrap_dataset(
  model,
  format = c("list", "dyno", "sce", "seurat", "anndata", "none"),
  store_dimred = !is.null(model$simulations$dimred),
  store_cellwise_grn = !is.null(model$experiment$cellwise_grn),
  store_rna_velocity = !is.null(model$experiment$rna_velocity)
)

Arguments

model: A dyngen output model for which the experiment has been emulated with generate_experiment().
store_dimred: Whether or not to store the dimensionality reduction constructed on the true counts.
store_cellwise_grn: Whether or not to also store cellwise GRN information.
store_rna_velocity: WHether or not to store the log propensity ratios.
format: Which output format to use, must be one of 'dyno' (requires dynwrap), 'sce' (requires SingleCellExperiment), 'seurat' (requires Seurat), 'anndata' (requires anndata), 'list' or 'none'.

Value

A dataset object.

Examples

data("example_model")
dataset <- wrap_dataset(example_model, format = "list")
# \donttest{
dataset <- wrap_dataset(example_model, format = "dyno")
#> Loading required namespace: dynwrap
dataset <- wrap_dataset(example_model, format = "sce")
#> Loading required namespace: SingleCellExperiment
dataset <- wrap_dataset(example_model, format = "seurat")
#> Loading required namespace: Seurat
dataset <- wrap_dataset(example_model, format = "anndata")
#> Loading required namespace: anndata
#> Error in py_module_import(module, convert = convert): ModuleNotFoundError: No module named 'anndata'
dataset <- wrap_dataset(example_model, format = "none")
# }