View source: R/generate_dataset.R
generate_dataset | R Documentation |
This function contains the complete pipeline for generating a dataset with dyngen. In order to have more control over how the dataset is generated, run each of the steps in this function separately.
generate_dataset( model, format = c("list", "dyno", "sce", "seurat", "anndata", "none"), output_dir = NULL, make_plots = FALSE, store_dimred = model$simulation_params$compute_dimred, store_cellwise_grn = model$simulation_params$compute_cellwise_grn, store_rna_velocity = model$simulation_params$compute_rna_velocity )
model |
A dyngen initial model created with |
format |
Which output format to use, must be one of 'dyno' (requires |
output_dir |
If not |
make_plots |
Whether or not to generate an overview of the dataset. |
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. |
A list containing a dyngen model (li$model
) and a dynwrap dataset (li$dataset
).
model <- initialise_model( backbone = backbone_bifurcating() ) # generate dataset and output as a list format # please note other output formats exist: "dyno", "sce", "seurat", "anndata" out <- generate_dataset(model, format = "list") model <- out$model dataset <- out$dataset
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