simulate-WGBSParam-method: Simulate a bisulfite-sequencing experiment.
In PeteHaitch/methsim: An R package to simulate DNA methylation data

Description Usage Arguments Value Warnings Note

Simulate a bisulfite-sequencing experiment.

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## S4 method for signature 'WGBSParam'
simulate(object, nsim = 1, seed = NULL, seqlevels,
  simplify = 0L, BPPARAM = bpparam())

`object`	A `WGBSParam` object.
`nsim`	The number of samples to simulate using the parameters given in `object`. Additional samples will be technical replicates.
`seed`	An object specifying if and how the random number generator should be initialized ('seeded'). For the "WGBSParam" method, either `NULL` or an integer that will be used in a call to `base::set.seed` before simulating the samples. If set, the value is saved as the "`seed`" attribute of the returned value. The default, `NULL`, will not change the random generator state, and return `.Random.seed` as the "`seed`" attribute, see 'Value'.
`seqlevels`	A character vector of `GenomeInfoDb::seqlevels` at which to bisulfite-sequencing reads. If missing, the default is to use all available seqlevels.
`simplify`	An integer specifying whether, and by how much, the object should be simplified, see 'Value'.
`BPPARAM`	an optional `BiocParallel::BiocParallelParam` instance determining the parallel back-end to be used during evaluation.

The return value depends on the value of simplify. The default (simplify = 0) means no simplification and the returned object is a list of length nsim containing SimulatedBS objects. If simplify is greater than zero, the returned object is a MethylationTuples::MethPat object with size = simplify and ncol = simplify.

Reads are not yet simulated for circular seqlevels such as 'chrM' (mitochondrial DNA).
Only single-end sequencing ('SE') is currently supported.
This is currently not RNG-safe since random numbers are generated within the parallel process and at the Rcpp level. Therefore, results may not be reproducible, even given the same seed. This is a work in progress and will be fixed.
The nsim simulations are currently simulated in serial (but steps of each simulation may be run in parallel).