makeExampleDESeqDataSet: Make a simulated DESeqDataSet

Description Usage Arguments Value Examples

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

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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

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DESeq2 documentation built on May 6, 2019, 3:53 a.m.