Hi,
To answer Steve's question first question ... yes. People (n = 1) are
indeed subsetting GRanges objects. In my case, I used
GRanges::subset() like this:
R> subset(tags, elementMetadata(tags)$genome.hits < 5 & strand(tag) ==
'+')
My question is, how does one discover that the singe-index square
bracket is implemented like this for GRanges? I didn't see any
mention of this in GenomicRanges.pdf of "?GRanges" .
Are there other methods that do not appear in the documentation, and
how can I learn about the existence of undocumented method in the
future?
Thx,
- Stu
Stuart Andrews, Ph.D.
Postdoctoral Associate
Institute for Computational Biomedicine
Weill Cornell Medical College, New York, NY
On Jun 4, 2010, at 9:18 PM, Michael Lawrence wrote:
On Fri, Jun 4, 2010 at 2:27 PM, Steve Lianoglou <
[email protected]> wrote:
Hi,
Random question I thought I'd shoot out there ...
I'm finding myself wanting to slice and dice IRanges-like objects
(I'm
playing with GRanges right now) based on some column of their
elementMetadata.
I guess if this makes sense then it would make sense to support this
for all
Sequence derivatives. It works already for RangedData, btw.
Michael
Are other people finding that they want to do this, too?
Would it make sense to add some subset-mojo to do that?
Here's a motivating example:
Say I have a GRanges object (`tags`), that looks something like:
GRanges with 2217486 ranges and 8 elementMetadata values
seqnames ranges strand | tag.id genome.hits
gene.hits
<Rle> <IRanges> <Rle> | <integer> <integer>
<integer>
[1] chr1 [ 4850, 4866] - | 405384
10 3
[2] chr1 [ 7804, 7820] - | 405387
6 4
[3] chr1 [13162, 13178] - | 405397
5 4
[4] chr1 [16712, 16728] + | 35 12164
2475
[5] chr1 [21381, 21397] + | 45
497 79
[6] chr1 [21479, 21495] - | 1466
3823 957
And say that I want all "tags" with < 5 genome.hits on the "+"
strand.
I'd like to:
R> subset(tags, genome.hits < 5 & strand == '+')
To do the same as:
R> tags[elementMetadata(tags)$genome.hits < 5 & strand(tag) == '+']
I realize that using `genome.hits` (from the elementMetadata) and
`strand` (not in the metadata) is crossing some boundaries, but I
just
wanted to point out one of the more "complex" cases.
Just curious,
-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<http://cbio.mskcc.org/%7Elianos/contact
>
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