srtsim_cci_free | R Documentation |
Generate Data with Cell-Cell Interaction Under Reference-Free Mode
srtsim_cci_free( zero_prop_in = 0, disper_in = Inf, mu_in = 1, numGene = 1000, location_in, region_cell_map, fc = 3, LR_in, sim_seed = 1, numKNN = 4, numSingleCellType = 2000 )
zero_prop_in |
A number specifying zero proportion for the count model, default is 0 |
disper_in |
A number specifying dispersion for the count model, default is Inf. Same as the size parameter in rnbinom. |
mu_in |
A number specifying mean for background count model, default is 1 |
numGene |
An integer specifying the number of genes in the synthetic data, default is 1000 |
location_in |
A dataframe with x, y, and region_label |
region_cell_map |
A dataframe specifying the cell type proportion in each region. Row: region,Column: cell type. |
fc |
A number specifying effect size for ligand-receptor pairs that mediate the cel-cell communication, default is 3 |
LR_in |
A dataframe specifying ligand and receptor pairs, containing four columns: protein_a, protein_b, celltypeA, and celltype B |
sim_seed |
A number for reproducible purpose |
numKNN |
A number specifying number of nearest neighbors with elevated gene expressin levels, default is 4 |
numSingleCellType |
A number specifying number of spots in the background pool. Gene expression count are then sampled from this background pool. |
Returns a SRTsim object with a newly generated count matrix and correspoding parameters
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