Description Usage Arguments Value Examples
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.
1 2 3  makeExampleDESeqDataSet(n = 1000, m = 12, betaSD = 0,
interceptMean = 4, interceptSD = 2, dispMeanRel = function(x) 4/x +
0.1, sizeFactors = rep(1, m))

n 
number of rows 
m 
number of columns 
betaSD 
the standard deviation for nonintercept 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

sizeFactors 
multiplicative factors for each sample 
a DESeqDataSet
with true dispersion,
intercept and beta values in the metadata columns. Note that the true
betas are provided on the log2 scale.
1 2  dds < makeExampleDESeqDataSet()
dds

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