mosim: mosim

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

mosim

Description

Performs a multiomic simulation by chaining two actions: 1) Creating the "MOSimulation" class with the provided params. 2) Calling "simulate" method on the initialized object.

Usage

mosim(
  omics,
  omicsOptions,
  diffGenes,
  numberReps,
  numberGroups,
  times,
  depth,
  profileProbs,
  minMaxFC,
  TFtoGene
)

Arguments

omics	Character vector containing the names of the omics to simulate, which can be "RNA-seq", "miRNA-seq", "DNase-seq", "ChIP-seq" or "Methyl-seq" (e.g. c("RNA-seq", "miRNA-seq")). It can also be a list with the omic names as names and their options as values, but we recommend to use the argument omicSim to provide the options to simulated each omic.
omicsOptions	List containing the options to simulate each omic. We recommend to apply the helper method omicSim to create this list in a friendly way, and the function omicData to provide custom data (see the related sections for more information). Each omic may have different configuration parameters, but the common ones are: simuData/idToGene Seed sample and association tables for regulatory omics. The helper function omicData should be used to provide this information (see the following section). regulatorEffect For regulatory omics. List containing the percentage of effect types (repressor, activator or no effect) over the total number of regulators. See vignette for more information. totalFeatures Number of features to simulate. By default, the total number of features in the seed dataset. depth Sequencing depth in millions of reads. If not provided, it takes the global parameter passed to mosim function. replicateParams List with parameters a and b for adjusting the variability in the generation of replicates using the negative binomial. See vignette for more information.
diffGenes	Number of differentially expressed genes to simulate, given in percentage (0 - 1) or in absolute number (> 1). By default 0.15
numberReps	Number of replicates per experimetal condition (and time point, if time series are to be generated). By default 3.
numberGroups	Number of experimental groups or conditions to simulate.
times	Vector of time points to consider in the experimental design.
depth	Sequencing depth in millions of reads.
profileProbs	Numeric vector with the probabilities to assign each of the patterns. Defaults to 0.2 for each.
minMaxFC	Numeric vector of length 2 with minimum and maximum fold-change for differentially expressed features, respectively.
TFtoGene	A logical value indicating if default transcription factors data should be used (TRUE) or not (FALSE), or a 3 column data frame containing custom associations. By default FALSE.

Value

Instance of class "MOSimulation" containing the multiomic simulation data.

Examples

 moSimulation <- mosim(
     omics = c("RNA-seq"),
     numberReps = 3,
     times = c(0, 2, 6, 12, 24)
 )

 # Retrieve simulated count matrix for RNA-seq
 dataRNAseq <- omicResults(moSimulation, "RNA-seq")

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