[Bioc-sig-seq] Simulating data

Hervé Pagès hpages at fhcrc.org
Wed Dec 8 21:11:24 CET 2010

Hi Jim,

On 12/03/2010 02:05 PM, Jim Silverton wrote:
> Hello,
> I want to simulate some RNA seq data and use fisher's exact test. Is there
> code available for this?

There is a simple/naive/non-realistic example of how to simulate reads
(not RNA-seq specific) in the man page of BSgenome::getSeq() function.

See ?getSeq, then look for the "D. EXTRACTING A HIGH NUMBER OF RANDOM
40-MERS FROM A GENOME" example. Just a starting point. To be more
realistic the code would need to be adapted to reflect the protocol
used and integrate experimental errors. Doesn't sound like a simple
task but maybe someone on the list already tried to do something like

> Secondly do you have the code for Tarone's Test and
> Gilbert's discrete FDR?

Someone else will know...


Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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