DESeq2: makeExampleDESeqDataSet – R documentation

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makeExampleDESeqDataSet

Make a simulated DESeqDataSet

Description

Constructs a simulated dataset of Negative Binomial data from two conditions. By default, there are no fold changes between the two conditions, but this can be adjusted with the betaSD argument.

Usage

makeExampleDESeqDataSet(
  n = 1000,
  m = 12,
  betaSD = 0,
  interceptMean = 4,
  interceptSD = 2,
  dispMeanRel = function(x) 4/x + 0.1,
  sizeFactors = rep(1, m)
)

Arguments

`n`	number of rows
`m`	number of columns
`betaSD`	the standard deviation for non-intercept betas, i.e. beta ~ N(0,betaSD)
`interceptMean`	the mean of the intercept betas (log2 scale)
`interceptSD`	the standard deviation of the intercept betas (log2 scale)
`dispMeanRel`	a function specifying the relationship of the dispersions on `2^trueIntercept`
`sizeFactors`	multiplicative factors for each sample

Value

a DESeqDataSet with true dispersion, intercept and beta values in the metadata columns. Note that the true betas are provided on the log2 scale.

Examples

dds <- makeExampleDESeqDataSet()
dds

DESeq2

Differential gene expression analysis based on the negative binomial distribution

v1.30.1

LGPL (>= 3)

Authors

Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Initial release