makeExampleDESeqDataSet: Make a simulated DESeqDataSet

View source: R/core.R

makeExampleDESeqDataSetR 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


mikelove/DESeq2 documentation built on July 25, 2024, 11:11 p.m.