makeExampleCountDataSet: make a simple example CountDataSet with random data

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

Description

This function returns an example CountDataSet. It is used for the examples in the package help pages.

Usage

makeExampleCountDataSet()

Value

a CountDataSet that has been constructed as follows: First, true base mean values for 10,000 genes are drawn from an exponential distribution with rate 1/250. Then, certain genes are declared (with probability 0.3 per gene) as truly differentially expressed (tDE). For these genes, the true base mean is split into two values, one for condition "A" and one for condition "B", such that the log2 fold change from "A" to "B" follows a zero-centred normal distribution with standard deviation 2. Then, counts are drawn for each gene for 5 samples, the first three corresponding to condition "A" and the remaining two for condition "B". The counts are drawn from a negative binomial with the specified mean, multiplied by the size factor for the sample, with a constant raw SCV (dispersion) of 0.2 (i.e., a 'size' parameter of 1/0.2). The true size factors are fixed to c( 1., 1.3, .7, .9, 1.6 ).

All these values were chosen to give data that at least somewhat resembles what one might encounter in an actual experiment. Note that this function is not meant to verify the package by simulation. For this purpose the parameters and distribution choices should be more varied.

Author(s)

Simon Anders, [e-mail]

Examples

    cds <- makeExampleCountDataSet()

DESeq documentation built on April 28, 2020, 6:37 p.m.