MOSimulator-class: Virtual class containing common methods and slots for child...
In Neurergus/MOSim: Multi-Omics Simulation (MOSim)

MOSimulator-class

R Documentation

Virtual class containing common methods and slots for child classes.

Description

Virtual class containing common methods and slots for child classes.

Slots

name: Name of the simulator to be used in messages.
data: Data frame containing the initial sample to be used, with the features IDs as rownames and only one column named "Counts".
regulator: Boolean flag to indicate if the omic is a regulator or not.
regulatorEffect: Possible regulation effects of the omic (enhancer, repressor or both).
idToGene: Data frame with the association table between genes and other features. The structure must be 2 columns, one named "ID" and the other "Gene".
min: Minimum value allowed in the omic.
max: Maximum value allowed in the omic.
depth: Sequencing depth to simulate.
depthRound: Number of decimal places to round when adjusting depth.
depthAdjust: Boolean indicating whether to adjust by sequencing depth or not.
totalFeatures: Number of features to simulate. This will replace the data with a subset.
noiseFunction: Noise function to apply when simulating counts. Must accept the parameter 'n' and return a vector of the same length. Defaults to 'rnorm'
increment: Read-only. Minimum value to increase when simulating counts.
simData: Contains the final simulated data.
pregenerated: Indicates if the child class will generate the simulated data instead of the general process.
randData: Auxiliary vector containing the original count data in random order with other adjustments.
noiseParams: Noise parameters to be used with noise function.
roundDigits: Number of digits to round the simulated count values.
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.
minMaxDist: Named list containing different minimum and maximum constraints values calculated at the beginning of the simulation process.
replicateParams: Named list containing the parameters a and b to be used in the replicates generation process, see the vignette for more info.