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Question: RNA-seq data simulation
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gravatar for Alpesh Querer
5.8 years ago by
Alpesh Querer220
Alpesh Querer220 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 [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Alpesh Querer220
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gravatar for Alpesh Querer
5.8 years ago by
Alpesh Querer220
Alpesh Querer220 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 > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.8 years ago by Alpesh Querer220
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 at="" 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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y11-J-16 w: http://tiny.cc/mrobin ---------- http://www.fgcz.ch/Bioconductor2012 http://www.eccb12.org/t5
ADD REPLYlink written 5.8 years ago by Mark Robinson870
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 > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > ---------- > Prof. Dr. Mark Robinson > Bioinformatics > Institute of Molecular Life Sciences > University of Zurich > Winterthurerstrasse 190 > 8057 Zurich > Switzerland > > v: +41 44 635 4848 > f: +41 44 635 6898 > e: mark.robinson@imls.uzh.ch > o: Y11-J-16 > w: http://tiny.cc/mrobin > > ---------- > http://www.fgcz.ch/Bioconductor2012 > http://www.eccb12.org/t5 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 5.8 years ago by Aaron Mackey160
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 > > >> > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > ---------- > > Prof. Dr. Mark Robinson > > Bioinformatics > > Institute of Molecular Life Sciences > > University of Zurich > > Winterthurerstrasse 190 > > 8057 Zurich > > Switzerland > > > > v: +41 44 635 4848 > > f: +41 44 635 6898 > > e: mark.robinson@imls.uzh.ch > > o: Y11-J-16 > > w: http://tiny.cc/mrobin > > > > ---------- > > http://www.fgcz.ch/Bioconductor2012 > > http://www.eccb12.org/t5 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 5.8 years ago by Marcus Davy390
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