yes, the chipseq vignette is great, I've already adapted and used the code, but as far as I understand the only way to identify peaks there is to use some sort of cut-off (e.g. define islands with a lower of xx, or a x-fold different coverage between sample to control). I'm interested in a way to calculate a p-value for the "enrichment" of the peak, taking the nr of reads and the depth into account.
On Mon, Mar 1, 2010 at 3:20 PM, Michael Lawrence <[email protected]>wrote: > > > On Mon, Mar 1, 2010 at 6:00 AM, Johannes Rainer < > [email protected]> wrote: > >> and in which package is it implemented? >> >> > The easiest place is in the chipseq package vignette. Just copy/paste and > adapt that code. > > > >> >> On Mon, Mar 1, 2010 at 2:39 PM, Michael Lawrence < >> [email protected]> wrote: >> >>> >>> >>> On Mon, Mar 1, 2010 at 5:25 AM, Martin Morgan <[email protected]>wrote: >>> >>>> On 03/01/2010 12:40 AM, Johannes Rainer wrote: >>>> > dear all, >>>> > >>>> > I'm just wondering if anybody has already implemented a ChIP-seq peak >>>> > detection algorithm (like MACS, PeakSeq...) or plans to do so. >>>> >>>> See http://bioconductor.org/packages/release/Software.html and search >>>> for chipseq, e.g., chipseq, ChIPseqR implement peak detection algorithms >>>> (though not MACS or PeakSeq; approximations of these algorithms are not >>>> difficult to implement using IRanges / Biostrings / ShortRead >>>> infrastructure). >>>> >>>> >>> Just to clarify, the chipseq package, while useful for chipseq in >>> general, does not implement a peak detection method. Deepayan's method is >>> implemented separately. >>> >>> >>>> Martin >>>> >>>> > >>>> > bests, jo >>>> > >>>> >>>> >>>> -- >>>> Martin Morgan >>>> Computational Biology / Fred Hutchinson Cancer Research Center >>>> 1100 Fairview Ave. N. >>>> PO Box 19024 Seattle, WA 98109 >>>> >>>> Location: Arnold Building M1 B861 >>>> Phone: (206) 667-2793 >>>> >>>> _______________________________________________ >>>> Bioc-sig-sequencing mailing list >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>>> >>> >>> >> >> >> -- >> Johannes Rainer, PhD >> Bioinformatics Group, >> Division Molecular Pathophysiology, >> Biocenter, Medical University Innsbruck, >> Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria >> and >> Tyrolean Cancer Research Institute >> Innrain 66, 6020 Innsbruck, Austria >> >> Tel.: +43 512 570485 13 >> Email: [email protected] >> [email protected] >> URL: http://bioinfo.i-med.ac.at >> >> > -- Johannes Rainer, PhD Bioinformatics Group, Division Molecular Pathophysiology, Biocenter, Medical University Innsbruck, Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria and Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria Tel.: +43 512 570485 13 Email: [email protected] [email protected] URL: http://bioinfo.i-med.ac.at [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
