Initial settings for simulating a dyngen dataset
initialise_model( backbone, num_cells = 1000, num_tfs = nrow(backbone$module_info), num_targets = 100, num_hks = 50, distance_metric = c("pearson", "spearman", "cosine", "euclidean", "manhattan"), tf_network_params = tf_network_default(), feature_network_params = feature_network_default(), kinetics_params = kinetics_default(), gold_standard_params = gold_standard_default(), simulation_params = simulation_default(), experiment_params = experiment_snapshot(), verbose = TRUE, download_cache_dir = getOption("dyngen_download_cache_dir"), num_cores = getOption("Ncpus") %||% 1L, id = NULL )
The gene module configuration that determines the type of dynamic
process being simulated. See
list_backbones() for a full list of different backbones
available in this package.
The number of cells to sample.
The number of transcription factors (TFs) to generate. TFs are the main drivers of the changes that occur in a cell. TFs are regulated only by other TFs.
The number of target genes to generate. Target genes are regulated by TFs and sometimes by other target genes.
The number of housekeeping genes (HKs) to generate. HKs are typically highly expressed, and are not regulated by the TFs or targets.
The distance metric to be used to calculate the distance
between cells. See
dynutils::calculate_distance() for a list of possible
Whether or not to print messages during the simulation.
NULL, temporary downloaded files will be
cached in this directory.
Parallellisation parameter for various steps in the pipeline.
An identifier for the model.
A dyngen model.
dyngen on how to run a complete dyngen simulation
model <- initialise_model( backbone = backbone_bifurcating(), num_cells = 555, verbose = FALSE, download_cache_dir = "~/.cache/dyngen" )