MOSimulator-class {MOSim} | 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.

[Package MOSim version 1.1.2 Index]