# Multi-Omics Simulation (MOSim)

## Documentation for package ‘MOSim’ version 2.7.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

associationList | Data to showcase scRNA and scATAC-seq association
calculate_mean_per_list_df | calculate_mean_per_list_df
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
match_gene_regulator | match_gene_regulator
match_gene_regulator_cluster | match_gene_regulator_cluster
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.
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 This function is a copy of the 'random_unif_interval' function from the 'SPARSim' package (v0.9.5), originally developed by Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo (2020). The original package is licensed under the GPL-3 license.
sampleData | Default data
scatac | Data to test scMOSim
scrna | Data to test scMOSim
sc_mosim | sc_mosim
sc_omicData | sc_omicData
sc_omicResults | sc_omicResults
sc_omicSettings | sc_omicSettings
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 This function is a slightly modified copy of the 'shuffle_group_matrix' function from the 'Acorde' package (v1.0.0), originally developed by Arzalluz-Luque A, Salguero P, Tarazona S, Conesa A. (2022). acorde unravels functionally interpretable networks of isoform co-usage from single cell data. Nature communications 1828. DOI: 10.1038/s41467-022-29497-w. The original package is licensed under the GPL-3 license.

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
TF_human | Data to extract human TF