[Bioc-sig-seq] peak calling/detection algorithm available in Bioconductor?

[Deepayan Sarkar]

On Mon, Mar 1, 2010 at 6:50 AM, Johannes Rainer
<johannes.rainer at i-med.ac.at> wrote:
> 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.

There is a fairly simple FDR calculation that's not in the vignette
yet; I'll try to put that in soon.

-Deepayan

>
>
> On Mon, Mar 1, 2010 at 3:20 PM, Michael Lawrence
> <lawrence.michael at gene.com>wrote:
>
>>
>>
>> On Mon, Mar 1, 2010 at 6:00 AM, Johannes Rainer <
>> johannes.rainer at i-med.ac.at> wrote:
>>
>>> and in which package is it implemented?
>>>
>>>
>> The easiest place is in the chipseq package vignette. Just copy/paste and
>> adapt that code.