[Bioc-sig-seq] release of chipseq package

[xiaoa]

I wonder if the chipseq package is available for the public. if not, 
what is the time line?-thanks, AX


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> Today's Topics:
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>    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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