MOSimulation-class: This class manages the global simulation process, like...

In Neurergus/MOSim: Multi-Omics Simulation (MOSim)

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.

Description

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.

Slots

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. Overwritten 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.

Neurergus/MOSim documentation built on Feb. 23, 2024, 8:29 a.m.