makeExampleDESeqDataSet {DESeq2} | R Documentation

## 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

[Package DESeq2 version 1.28.1 Index]