makeComplexDESeqData: Make a simulated DESeqDataSet with a potentially complex...

In baj12/crtRNAtools: Toolbox for RNAseq and scRNAseq projects

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

makeComplexDESeqData(n = 1000, m = 24, betaSD = 0, interceptMean = 4,
  interceptSD = 2, designStr = "~ condition1 + condition2",
  dispMeanRel = function(x) 4/x + 0.1, sizeFactors = rep(1, m))

Arguments

n	number of rows (should be a multiple of 4)
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)
designStr	design string one of "~ condition1 + condition2" , "~ condition1 * condition2", "~ condition1"
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 <- makeComplexDESeqData()
dds

baj12/crtRNAtools documentation built on May 14, 2019, 2 a.m.