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Simulate true scRNA and scATAC counts from the parameters

Source: R/1_main.R
sim_true_counts.Rd

Simulate true scRNA and scATAC counts from the parameters

Usage

sim_true_counts(options)

Arguments

options

See scMultiSim_help().

Value

scMultiSim returns an environment with the following fields:

  • counts: Gene-by-cell scRNA-seq counts.

  • atac_counts: Region-by-cell scATAC-seq counts.

  • region_to_gene: Region-by-gene 0-1 marix indicating the corresponding relationship between chtomatin regions and genes.

  • atacseq_data: The "clean" scATAC-seq counts without added intrinsic noise.

  • cell_meta: A dataframe containing cell type labels and pseudotime information.

  • cif: The CIF used during the simulation.

  • giv: The GIV used during the simulation.

  • kinetic_params: The kinetic parameters used during the simulation.

  • .grn: The GRN used during the simulation.

  • .grn$regulators: The list of TFs used by all gene-by-TF matrices.

  • .grn$geff: Gene-by-TF matrix representing the GRN used during the simulation.

  • .n: Other metadata, e.g. .n$cells is the number of cells.

If do.velocity is enabled, it has these additional fields:

  • unspliced_counts: Gene-by-cell unspliced RNA counts.

  • velocity: Gene-by-cell RNA velocity ground truth.

  • cell_time: The pseudotime at which the cell counts were generated.

If dynamic GRN is enabled, it has these additional fields:

  • cell_specific_grn: A list of length n_cells. Each element is a gene-by-TF matrix, indicating the cell's GRN.

If cell-cell interaction is enabled, it has these additional fields:

  • grid: The grid object used during the simulation.

    • grid$get_neighbours(i): Get the neighbour cells of cell i.

  • cci_locs: A dataframe containing the X and Y coordinates of each cell.

  • cci_cell_type_param: A dataframe containing the CCI network ground truth: all ligand-receptor pairs between each pair of cell types.

  • cci_cell_types: For continuous cell population, the sub-divided cell types along the trajectory used when simulating CCI.

If it is a debug session (debug = TRUE), a sim field is available, which is an environment contains all internal states and data structures.

Examples

data(GRN_params_100, envir = environment())
sim_true_counts(list(
  rand.seed = 0,
  GRN = GRN_params_100,
  num.cells = 1000,
  num.cifs = 50,
  tree = Phyla5()
))
#> Time spent: 0.09 mins
#> <environment: 0x34b0de108>
#> attr(,"name")
#> [1] "scMultiSim Result"