MOSimulation-class: This class manages the global simulation process, like...
In MOSim: Multi-Omics Simulation (MOSim)

Description Slots

This class manages the global simulation process, like associating genes with gene classes, regulatory programs and other settings. Finally it will initialize the simulators with their options that will use the previously generated settings to simulate the data.

simulators: Vector containing either S4 initialized classes of simulators or a list with the class name as keys, and its options as value, see example.
totalGenes: A number with the total number of genes including not expressed. Overwrited if a genome reference is provided. Currently not used as we force to provide real data.
diffGenes: A number with the total number of differential genes (if value > 1) or % or total genes (if value < 1).
numberReps: Number of replicates of the experiment.
numberGroups: Number of samples considered on the experiment.
times: Numeric vector containing the measured times. If numberGroups < 2, the number of times must be at least 2.
geneNames: Read only. List containing the IDs of the genes. Overwrited by the genome reference if provided. Currently not used as we force to provide real data.
simSettings: List of settings that overrides initializing the configuration of the simulation by passing a previously generated list. This could be used to tweak by hand the assigned profiles, genes, regulatory programs, etc.
noiseFunction: Noise function to apply when simulating counts. Must accept the parameter 'n' and return a vector of the same length. Defaults to 'rnorm'
profiles: Named list containing the patterns with their coefficients.
profileProbs: Numeric vector with the probabilities to assign each of the patterns. Defaults to 0.2 for each.
noiseParams: Default noise parameters to be used with noise function.
depth: Default depth to simulate.
TFtoGene: Boolean (for default data) or 3 column data frame containing Symbol-TFGene-LinkedGene
minMaxQuantile: Numeric vector of length 2 indicating the quantiles to use in order to retrieve the absolute minimum and maximum value that a differentially expressed feature can have.
minMaxFC: Numeric vector of length 2 indicating the minimum and maximum fold-change that a differentially expressed feature can have.