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