Gabe - very cool! I'll be following this with interest.
Ryan - conceptually I haven't been thinking of fixed-width ranges as
different from general ranges, hence why I think it'd be neat if the
user just got the benefits of space-efficient representation without
having to know/care about the under
Hi all,
In addition to the technical concerns, I suppose we should consider
whether fixed-width ranges are conceptually different enough from
general ranges to warrant a separate class, or whether this is just
being considered for purely technical reasons. My feeling is that
fixed-width range
Hey all,
I just wanted to chime in on this as it relates to some work I'm doing with
Luke Tierney and Tomas Kalibera. There's another approach to this that will
be available in the near future (we hope).
Alternative internal representations of atomic vectors, including compact
representations, ar
Is it possible to allow the width slot of IRanges to be either a normal
vector or an Rle?
On 11/23/16 6:18 PM, Peter Hickey wrote:
I've been toying with the idea of a fixed/constant width Ranges
subclass. The motivation comes from storing DNA methylation data at CH
loci (non-CpG methylation):
Vince - From my understanding GPos mostly gains its efficiencies when
positions are adjacent, which is generally not the case for the types of
positions I'm considering. In fact, the @ranges slot of the @pos_runs slot
in a GPos object is just a IRanges object where n adjacent positions are
'compres
pace Wolfgang Huber ...
Peter I don't mean to be rude. Your comments deserve more study. But it
was fun to remember GPos, which I had forgotten.
On Wed, Nov 23, 2016 at 6:34 PM, Vincent Carey
wrote:
> library(GenomicRanges)
> class?GPos
>
> On Wed, Nov 23, 2016 at 6:18 PM, Peter Hickey
> wro
library(GenomicRanges)
class?GPos
On Wed, Nov 23, 2016 at 6:18 PM, Peter Hickey
wrote:
> I've been toying with the idea of a fixed/constant width Ranges
> subclass. The motivation comes from storing DNA methylation data at CH
> loci (non-CpG methylation): there are 1.1 billion CH loci in the hum
I've been toying with the idea of a fixed/constant width Ranges
subclass. The motivation comes from storing DNA methylation data at CH
loci (non-CpG methylation): there are 1.1 billion CH loci in the human
genome, so to store these as a GRanges object requires 2 x 1.1 billion
integer vectors, one f
