Hi Dario,
On 02/16/2016 03:00 AM, Dario Strbenac wrote:
Hello,
There is no convenience function to sample nucleotide positions from a GRanges
object. My approach is to generate a GRanges of every chromosomal position with
a width of 1, then find the overlaps with the desired ranges (admissibl
Hi Kasper,
On 02/16/2016 07:05 AM, Kasper Daniel Hansen wrote:
upstream / downstream is what we have previously used for strand awareness.
These names are good for specifying *relative* positions in a
way that is strand-aware. In the case of restrict() though, where we
need to be able to speci
Hi Dario,
You could use a package called regioneR for that. It has functions to
create random regions and to randomize existing sets of regions along
the genome and it can do it taking into account a possible set of masked
regions.
In your case, you could create a mask for the genome that is
I have answered your email in the tracker, twice. Please do not reply all to
random threads on bioc-devel.
On February 16, 2016 8:41:25 AM PST, Yuande Tan wrote:
>Dear all:
>Today I resubmit the revised version of MBttest with fix error
>occurring in
>building windows. Right now I received mes
Dear all:
Today I resubmit the revised version of MBttest with fix error occurring in
building windows. Right now I received message from SinglePackageBuilder
BioC-Submit. It said one or more warnings in build. I checked the History
Biocond Single Builder, the warnings list in morelia and moscato2
upstream / downstream is what we have previously used for strand awareness.
Kasper
On Tue, Feb 16, 2016 at 3:41 AM, Hervé Pagès wrote:
> Hi Dario,
>
> AFAIK the 'start' and 'end' are strand-independent concepts so it
> wouldn't be a good idea to let the user specify a strand-specific
> window t
Hi Michael,
Thanks for the suggestion. When I depend my package on GenomicRanges the
warning is now gone.
Regards,
Andreas
--
Chantriolnt - Andreas Kapourani
PhD Candidate in Data Science,
School of Informatics,
University of Edinburgh
e-m
Hello,
There is no convenience function to sample nucleotide positions from a GRanges
object. My approach is to generate a GRanges of every chromosomal position with
a width of 1, then find the overlaps with the desired ranges (admissible
regions), then sample the positions that overlapped. The
Hi Dario,
AFAIK the 'start' and 'end' are strand-independent concepts so it
wouldn't be a good idea to let the user specify a strand-specific
window thru these arguments. That means a strand-aware restrict()
would need to have 2 additional arguments. But how should we name them?
My preference wo
