makeExampleDESeqDataSet: Make a simulated DESeqDataSet

In DESeq2: Differential gene expression analysis based on the negative binomial distribution

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 documentation built on Feb. 22, 2021, 10 a.m.