simulateGEx: Simulate observed gene expression data for a set of samples
In stephaniehicks/quantroSim: Supporting Data Simulation R-package for quantro

Description Usage Arguments Value Author(s) Examples

This function simulates observed gene expression data based on the set of platforms listed in list.GEx.platforms. The gene expression arrays are simulated using the Langmuir adsorption model.

simulateGEx(simulateGExTruthObject, GEx.platform = "GExArrays", nSamps,
  usePCR = FALSE, nPCRcycles = 15, verbose = TRUE, mua = NULL,
  siga = NULL, mub = NULL, sigb = NULL, muOpt = NULL, sigOpt = NULL,
  muBG = NULL, sigBG = NULL, muERR = NULL, sigERR = NULL)

`simulateGExTruthObject`	Must be an object created from `simulateGExTruth`.
`GEx.platform`	Must specify a platform from `list.GEx.platforms`.
`nSamps`	number of samples in each group
`usePCR`	TRUE/FALSE option. Default is FALSE. If TRUE, amplify RNA fragments with PCR.
`nPCRcycles`	number of PCR cycles. Default is 15.
`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

A list of elements

`objectType`	a string specifying the type of object.
`typePlatform`	platform used to simulate the gene expression.
`usePCR`	A TRUE/FALSE object specifying if PCR was used to amplify the RNA counts.
`nGenes`	number of genes
`nProbes`	number of probes
`nSamps`	number of samples
`nGroups`	number of groups
`params`	list of elements reported from `pickLangmuirParameters`
`geneNames`	gene names (or probeset names)
`nProbesPerGene`	number of probes per gene (or probeset)
`pd`	phenoData containing information about the simulated samples
`PM`	the simulated gene expression data

Stephanie Hicks

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geneTruth <- simulateGExTruth(nGenes = 2e4, nGroups = 2,
                             pDiff = 0.05, foldDiff = 5)
sim <- simulateGEx(geneTruth, GEx.platform = "GExArrays", nSamps = 5)