simulateGExTruth: Simulate true gene expression 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 gene expression data. The gene expression arrays are simulated using a zero inflated log-normal poisson distribution to represent the number or RNA molecules in a sample.

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simulateGExTruth(nGenes, nGroups = 2, muHyp = NULL, sigHyp = NULL,
  zeroWeight = 0.1, pDiff = 0.05, foldDiff = 5, scaleCounts = 1,
  verbose = TRUE)

`nGenes`	number of genes to simulate.
`nGroups`	number of groups. Default is 2.
`muHyp`	hyperparameters for mean of log normal. See `pickLogNormal` for default values.
`sigHyp`	hyperparameters for variance of log normal. See `pickLogNormal` for default values.
`zeroWeight`	proportion of zero-inflated counts. Default is 0.10.
`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`.
`foldDiff`	fold difference relative to Group 1. If `nGroups == 1`, foldDiff is ignored. If `nGroups > 1`, the length of foldDiff should be equal to `nGroups - 1`. Default is `foldDiff = 5`.
`scaleCounts`	To plot gene expression on log2 scale, pick a small amount to scale the counts by. Default is 1.
`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.
`nGenes`	Number of genes simulated.
`zeroWeight`	Proportion of zero-inflated counts used in simulation.
`pDiff`	Percent of probes different relative to Group 1.
`foldDiff`	fold difference relative to Group 1.
`scaleCounts`	An positive real valued number specifying an additive scale for the RNA counts to be able to plot on the log2 scale.
`genesDiffInd`	Boolean array referencing which probes are different relative to Group 1.
`geneRange`	Data frame containing the simulated RNA molecules for each gene and for each group.