[Bioc-sig-seq] Add ability for `subset`ing IRanges-like objects based on their elementMetadata?

[Steve Lianoglou]

Hi Vincent,

> the simplification that Steve
> seems to be asking for would
> allow implicit references to elementMetadata variables in the predicate.  I
> am not in favor of such
> an extension of semantics of bracket.

Just to be clear, I'm not suggesting referencing elementMetadata
variables implicitly w/in brackets, but rather only when using
`subset` (as `subset` does now with columns of a data.frame (when it's
used *on* a data.frame))

So, using your example gr object:

GRanges with 10 ranges and 2 elementMetadata values
 seqnames    ranges strand |     score        GC
    <Rle> <IRanges>  <Rle> | <integer> <numeric>
a   Chrom1  [ 1, 10]      - |         1 1.0000000
b   Chrom2  [ 2, 10]      + |         2 0.8888889
c   Chrom2  [ 3, 10]      + |         3 0.7777778
d   Chrom2  [ 4, 10]      * |         4 0.6666667
e   Chrom1  [ 5, 10]      * |         5 0.5555556
f   Chrom1  [ 6, 10]      + |         6 0.4444444
g   Chrom3  [ 7, 10]      + |         7 0.3333333
h   Chrom3  [ 8, 10]      + |         8 0.2222222
i   Chrom3  [ 9, 10]      - |         9 0.1111111
j   Chrom3  [10, 10]      - |        10 0.0000000

seqlengths
 Chrom1 Chrom2 Chrom3
    NA     NA     NA

I was curious if this would be useful:

R> subset(gr, strand == "+" & score > 6)

but I wasn't trying to propose having something like this:

R> gr[strand == "+" & score > 6]

-- 
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