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> > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
