simulateMethTruth: Simulate true DNA methylation data for a set of groups
In stephaniehicks/quantroSim: Supporting Data Simulation R-package for quantro

Description Usage Arguments Value Author(s) See Also Examples

This function simulates true DNA methylation data. The true DNA methylation data is simulated using a mixture of three normal distributions to represent a probe that is not methylated, semi-methylated and methylated. To scale the values between 0 and 1, the values are transformed using an inverse-logit transformation. These scaled values represent the true proportion of methylation at each probe.

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simulateMethTruth(nProbes, nGroups = 2, nMixtures = 3,
  propMixtures = NULL, muMixtures = NULL, sigMixtures = NULL,
  pDiff = 0.05, pUp = 0.8, verbose = TRUE)

`nProbes`	number of probes
`nGroups`	number of groups. Default is 2.
`nMixtures`	number of normal distributions to simulate. Default is 3. Can be changed, but user must then supply mixing proportions (propMixtures), mean (muMixtures) and variance (sigMixtures).
`propMixtures`	weights or mixture proportions for the normal distributions. Should be a vector of length nMixtures. See `pickNormalMix` for default values.
`muMixtures`	mean of the normal distributions. Should be a vector of length nMixtures. See `pickNormalMix` for default values.
`sigMixtures`	variance of the three normal distributions. Should be a vector of length nMixtures. See `pickNormalMix` for default values.
`pDiff`	percent of probes different relative to Group 1. If `nGroups == 1`, pDiff should be 0. If `nGroups > 1`, the length of pDiff should be equal to `nGroups - 1`. Default is `pDiff = 0.05`.
`pUp`	proportion of pDiff probes that are methylated relative to Group 1. If `nGroups == 1`, pUp is ignored. If `nGroups > 1`, the length of pUp should be equal to `nGroups - 1`. Default is `pUp = 0.80`.
`verbose`	TRUE/FALSE argument specifying if verbose messages should be returned or not. Default is TRUE.

A list with elements

`objectType`	A string specifying the type of object.
`nProbes`	Number of probes.
`nGroups`	Number of groups.
`trueParams`	Add me.
`simObs`	Add me.
`methDiffInd`	Add me.
`methRange`	Add me.