great, thanks!!
robert.
On 02/25/2015 10:06 PM, Michael Lawrence wrote:
I checked in a fix for the splitting to CompressedVRangesList. The
slowness of creating a SimpleVRangesList is due to the cost of
extracting a VRanges for each sample. Depending your exact use case, it
might be better to pa
I checked in a fix for the splitting to CompressedVRangesList. The slowness
of creating a SimpleVRangesList is due to the cost of extracting a VRanges
for each sample. Depending your exact use case, it might be better to pay
that cost up-front, instead of deferring it to when the user wants to
extr
Yea, I know, just need to get around to that one. Technically, it works,
but it's obviously not ideal.
On Wed, Feb 25, 2015 at 8:52 AM, Gabe Becker wrote:
> Why does splitting a VRanges give a GRangesList with VRanges objects as
> elements? Seems like it should return a VRangesList.
>
> > spl =
Why does splitting a VRanges give a GRangesList with VRanges objects as
elements? Seems like it should return a VRangesList.
> spl = split(vr, sampleNames(vr))
> class(spl)
[1] "GRangesList"
attr(,"package")
[1] "GenomicRanges"
> class(spl[[1]])
[1] "VRanges"
attr(,"package")
[1] "VariantAnnotatio
Construction will take longer; the savings are in the accessing of the
elements. But this seems like too much longer, so I will look into it.
On Wed, Feb 25, 2015 at 8:12 AM, Robert Castelo
wrote:
> my current reason to prefer a CompressedVRangesList object over a
> SimpleVRangesList object is t
my current reason to prefer a CompressedVRangesList object over a
SimpleVRangesList object is that i find one order of magnitude
difference in creation time in each of these classes of objects:
library(VariantAnnotation)
fl <- system.file("extdata", "CEUtrio.vcf.bgz",
package
If you're storing data on a relatively small number of individuals (say,
hundreds), you should use SimpleVRangesList, not CompressedVRangesList.
On Wed, Feb 25, 2015 at 7:10 AM, Robert Castelo
wrote:
> i see you point, the logic i was thinking about is to use a list of
> VRanges objects to hold
i see you point, the logic i was thinking about is to use a list of
VRanges objects to hold separately the variants of multiple individuals,
with one VRanges object per individual.
if i type the name of such a list object on the R shell, having the
GRangesList show method, i feel i do not see
Why not have the SimpleVRangesList be shown like CompressedVRangesList, for
consistency with GRangesList? In other words, the opposite of what you
propose. A strong argument could also be made that a
SimpleGenomicRangesList should be shown like a GRangesList. Unless there is
some aversion to the mo
so, yes, but IMO rather than inheriting the show method from a
GRangesList, i think that the show method for CompressedVRangesList
objects should be inherited from a VRangesList object. right now this is
the situation:
library(VariantAnnotation)
example(VRangesList)
vrl
VRangesList of length 2
I think you might be missing an import. It should inherit the method for
GRangesList.
On Tue, Feb 24, 2015 at 9:53 AM, Robert Castelo
wrote:
> hi,
>
> i'm using the CompressedVRangesList class in VariantFiltering to hold
> variants and their annotations across multiple samples and found that the
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