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
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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 <[email protected]>
Subject: [Bioc-sig-seq] AlignedRead and complex subsetting
To: [email protected]
Message-ID:
<[email protected]>
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 <[email protected]>
Subject: Re: [Bioc-sig-seq] AlignedRead and complex subsetting
To: Ivan Gregoretti <[email protected]>
Cc: [email protected]
Message-ID: <[email protected]>
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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