There is also

 DESeq::makeExampleCountDataSet

in the DESeq package. You could modify the function which currently doesn't
contain any input args for the number of genes, biological replicates or
pi0, proportion of truely null hypotheses.

Marcus


On Wed, Aug 22, 2012 at 5:28 AM, Aaron Mackey <amackey@virginia.edu> wrote:

> Try FluxSimulator, or BEERS, both mentioned in this thread:
>
>   http://seqanswers.com/forums/showthread.php?t=5386
>
> -Aaron
>
> On Tue, Aug 21, 2012 at 11:00 AM, Mark Robinson
> <mark.robinson@imls.uzh.ch>wrote:
>
> >
> > You could start with rnbinom().  The 'size' argument is 1/dispersion.
> >
> > Mark
> >
> > On 21.08.2012, at 16:51, Alpesh Querer wrote:
> >
> > > I should mention I want to use negative binomial as underlying
> > distribution.
> > >
> > > Thanks.
> > > Al
> > >
> > > On Tue, Aug 21, 2012 at 9:41 AM, Alpesh Querer <alpeshq@gmail.com>
> > wrote:
> > >
> > >> Hi all,
> > >>
> > >> I want to simulate counts for 1000 genes for 5 RNA-seq samples (with 3
> > >> biological replicates each), and I want to provide the dispersion
> > >> parameters myself.
> > >> Is there a package or code that can help me do this?
> > >>
> > >> Thanks a lot for your help,
> > >> Al
> > >>
> > >
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> > University of Zurich
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