convert: Convert simulation output to different formats.

In dyngen: A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses

Convert simulation output to different formats.

Description

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

Usage

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")

dataset <- wrap_dataset(example_model, format = "dyno")
dataset <- wrap_dataset(example_model, format = "sce")
dataset <- wrap_dataset(example_model, format = "seurat")
dataset <- wrap_dataset(example_model, format = "anndata")
dataset <- wrap_dataset(example_model, format = "none")

dyngen documentation built on Oct. 12, 2022, 5:06 p.m.