simulateMeth: Simulate observed DNA methylation data for a set of samples

In stephaniehicks/quantroSim: Supporting Data Simulation R-package for quantro

Description

This function simulates observed DNA methylation data based on the set of platforms listed in list.meth.platforms. The DNA methylation is simulated using the Langmuir adsorption model.

Usage

simulateMeth(simulateMethTruthObject, meth.platform, nSamps, nMol = NULL,
  verbose = TRUE, mua = NULL, siga = NULL, mub = NULL, sigb = NULL,
  muOpt = NULL, sigOpt = NULL, muBG = NULL, sigBG = NULL,
  muERR = NULL, sigERR = NULL)

Arguments

simulateMethTruthObject	Must be an object created from simulateMethTruth.
meth.platform	Must specify a platform from list.meth.platforms.
nSamps	number of samples in each group
nMol	number of molecules after amplification
verbose	TRUE/FALSE option to print details about simulation. Default is TRUE.
mua	hyperparameter: mean of log normal distribution for a
siga	hyperparameter: variance of log normal distribution for a
mub	b hyperparameter: mean of log normal distribution for b
sigb	b hyperparameter: variance of log normal distribution for b
muOpt	hyperparameter: mean of log normal distribution for optical noise
sigOpt	hyperparameter: variance of log normal distribution for optical noise
muBG	hyperparameter: mean of log normal distribution for d
sigBG	hyperparameter: variance of log normal distribution for d
muERR	hyperparameter: mean of log normal distribution for measurement error
sigERR	hyperparameter: variance of log normal distribution for measurement error

Value

A list of elements

objectType	a string specifying the type of object.
typePlatform	platform used to simulate the gene expression.
nProbes	number of probes
nSamps	number of samples
nGroups	number of groups
params	list of elements reported from pickLangmuirParameters
pd	phenoData containing information about the simulated samples
meth	the simulated raw methylated data
unmeth	the simulated raw unmethylated data

Author(s)

Stephanie Hicks

Examples

methTruth <- simulateMethTruth(nProbes = 2e4, nGroups = 2,
                               pDiff = 0.05, pUp = 0.80)
sim <- simulateMeth(methTruth, meth.platform = "methArrays",
                    nSamps = 5, nMol = 10^6)

stephaniehicks/quantroSim documentation built on May 30, 2019, 3:17 p.m.