On Fri, Jun 4, 2010 at 2:27 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> 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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