[Bioc-sig-seq] release of chipseq package

[Patrick Aboyoun]

The chipseq package is available for the BioC 2.5/R-devel (2.10) code 
line. You can download it via the normal biocLite method.


Cheers,
Patrick


xiaoa wrote:
> I wonder if the chipseq package is available for the public. if not, 
> what is the time line?-thanks, AX
>
>
> ioc-sig-sequencing-request at r-project.org wrote:
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>> Today's Topics:
>>
>>    1. AlignedRead and complex subsetting (Ivan Gregoretti)
>>    2. Re: AlignedRead and complex subsetting (Steve Lianoglou)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 31 Aug 2009 16:54:06 -0400
>> From: Ivan Gregoretti <ivangreg at gmail.com>
>> Subject: [Bioc-sig-seq] AlignedRead and complex subsetting
>> To: bioc-sig-sequencing at r-project.org
>> Message-ID:
>>     <a394a9180908311354m356bafbfsb94bea27109c8ba6 at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hello Everybody,
>>
>> How do you subset an AlignedRead instance to keep (or reject) tags
>> that lay within a set of genomic regions?
>>
>>
>> Example
>>
>> Lets say that I have an AlignedRead instance called aln.
>>
>> Now let's say that I have a set of positions in BED style:
>>
>> (chromosome, start end)
>> ch1 1000000 1000050
>> chrX 20000000 20100000
>> ...(many more)...
>>
>> We can imagine that I have the BED set loaded as a data frame.
>>
>> Is it possible to pick from aln only the tags within (or outside) the
>> features defined in the table described above?
>>
>> Thank you,
>>
>> Ivan
>>
>>
>> Ivan Gregoretti, PhD
>> National Institute of Diabetes and Digestive and Kidney Diseases
>> National Institutes of Health
>> 5 Memorial Dr, Building 5, Room 205.
>> Bethesda, MD 20892. USA.
>> Phone: 1-301-496-1592
>> Fax: 1-301-496-9878
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 31 Aug 2009 18:53:58 -0400
>> From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
>> Subject: Re: [Bioc-sig-seq] AlignedRead and complex subsetting
>> To: Ivan Gregoretti <ivangreg at gmail.com>
>> Cc: bioc-sig-sequencing at r-project.org
>> Message-ID: <1DA771DA-9E30-489D-ABFC-CC1C221A0DA9 at gmail.com>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> Hi Ivan,
>>
>> On Aug 31, 2009, at 4:54 PM, Ivan Gregoretti wrote:
>>
>>  
>>> Hello Everybody,
>>>
>>> How do you subset an AlignedRead instance to keep (or reject) tags
>>> that lay within a set of genomic regions?
>>>
>>>
>>> Example
>>>
>>> Lets say that I have an AlignedRead instance called aln.
>>>
>>> Now let's say that I have a set of positions in BED style:
>>>
>>> (chromosome, start end)
>>> ch1 1000000 1000050
>>> chrX 20000000 20100000
>>> ...(many more)...
>>>
>>> We can imagine that I have the BED set loaded as a data frame.
>>>
>>> Is it possible to pick from aln only the tags within (or outside) the
>>> features defined in the table described above?
>>>     
>>
>> I think that you should convert your BED file to an IRanges object,  
>> and use overlap with your ranges + your readAligned object to get 
>> what  your after. See Martin's post about something like this in this 
>> thread:
>>
>> https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2009-August/000509.html 
>>
>>
>> To get the reads *outside* of your ranges, maybe you can call the  
>> ``gaps`` on your bed/ranges and then do the same thing ...  or  
>> perhaps  ``setdiff(ranges, aln)`` might work, too? (where aln is 
>> your  IRanges converted alignedRead object (if necessary)).
>>
>> -steve
>>
>> -- 
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>    |  Memorial Sloan-Kettering Cancer Center
>>    |  Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
>>
>>
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>> End of Bioc-sig-sequencing Digest, Vol 19, Issue 1
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