Multi-Omics Simulation (MOSim)

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Documentation for package ‘MOSim’ version 2.3.0

• 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