Multi-Omics Simulation (MOSim)
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Documentation for package ‘MOSim’ version 2.0.0
Help Pages
| associationList | Data to showcase scRNA and scATAC-seq association |
| check_patterns | check_patterns |
| discretize | Discretize ChIP-Seq counts to simulate a binary dataset |
| experimentalDesign | Retrieves the experimental design |
| is.declared | Check if a variable is declared. |
| make_association_dataframe | make_association_dataframe |
| make_cluster_patterns | make_cluster_patterns |
| mosim | mosim |
| omicData | Set customized data for an omic. |
| omicResults | Retrieves the simulated data. |
| omicSettings | Retrieves the settings used in a simulation |
| omicSim | Set the simulation settings for an omic. |
| order_FC_forMatrix | order_FC_forMatrix |
| plotProfile | Generate a plot of a feature's profile for one or two omics. |
| random_unif_interval | random_unif_interval Function to call the C code |
| sampleData | Default data |
| scatac | Data to test scMOSim |
| scMOSim | scMOSim |
| scOmicResults | scOmicResults |
| scOmicSettings | scOmicSettings |
| scrna | Data to test scMOSim |
| sc_omicData | sc_omicData |
| sc_param_estimation | sc_param_estimation |
| shuffle_group_matrix | shuffle_group_matrix, Reorder cell type-specific expression matrix during co-expression simulation. Copied from ACORDE (https://github.com/ConesaLab/acorde) to facilitate stability and running within our scripts |
| simulate_coexpression | simulate coexpression |
| simulate_hyper | Simulate technical variability |
| sparsim_create_simulation_parameter | Create SPARSim simulation parameter |
| sparsim_estimate_intensity | Estimate SPARSIm "intensity" parameter |
| sparsim_estimate_library_size | Estimate SPARSim "library size" parameter |
| sparsim_estimate_parameter_from_data | Estimate SPARSim simulation parameter from a given count table |
| sparsim_estimate_variability | Estimate SPARSim "variability" parameter |
| sparsim_simulation | Function to simulate a raw count table |