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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