Hi Luke,
Do you mean bins or bin pairs?
If you want to just bin the coverage in terms of the linear genome,
there should be ways to do that outside of InteractionSet or
GenomicInteractions. This is just dealing with standard genomic interval
data; extract the anchor coordinates and plug it in
Maybe the question arises whether to store a reduced representation like, say,
singleCellExperiment does?
In any event, I agree that endomorphism will be expected by users and, like
tximport collapsing many transcripts into each gene, the sensible thing to do
is just to return a binned (less ro
Why is this not "just" a function which transforms one GI into another GI?
Thats what it seems to me.
On Fri, Mar 22, 2019 at 12:31 PM Luke Klein wrote:
> I am writing a package that will extend the GenomicInteractions class. I
> am a statistician, so I may not know best practices when it comes
Hi Koustav,
From a Build System point of view, we certainly don't want packages to
write files to the user's home (or to the current directory, which might
be different from the user's home) during 'R CMD build' and 'R CMD
check'. (Note that there is actually no guarantee that the current
dir
In response to Vince’s comment:
My package already has an implementation for checking if the file exists and
then to explicitly require the user’s permission for removing the file
In response to Lori’s comment:
In my implementation of BiocFileCache, if a user provides a filename without an
exp
I am writing a package that will extend the GenomicInteractions class. I am a
statistician, so I may not know best practices when it comes to extending
existing classes (eg. should I make a new slot or simply add a column to the
`elementMetadata`? Are there existing functions that already do w
Dear all,
if I understand correctly, the main problem stems from the fact that the
function has set a default value for "Output.Filename” argument.
Would it then be ok to have NO default value for Output.Filename? So as to
force the user to specify one
Or alternatively, the solution adopt
To chime and expand a bit on Vince's comments:
I feel Bioconductor's position when accepting packages , with few exceptions,
is that nothing should be written or saved to a users directory without the
expressed permission of the user for fear of overwriting a users own directory
or files prev
Guidelines on this topic do not seem to be present in our web
site; there is a link to Wickham's guide but I don't see that it
confronts the topic. I will make some unofficial and possibly
wrong remarks.
Suppose my function has to create a file "foo.txt". If I do it
in the working folder, I migh
Hello,
My package HiCBricks was submitted and accepted under the previous 3.8 release
of Bioconductor.
At the time, during package review, my reviewer had expressed reservations
towards my package creating
files in the current working directory.
[REQUIRED] CreateLego() creates HDF5 files in
The final day to submit new packages to the Bioconductor contributions tracker
to have a shot at being included in the upcoming 3.9 release is Friday April
5th.
Please note: submission by this date does not guarantee it will be included -
the package must undergo an official review and be accep
Hi all,
The release of Bioconductor 3.9 will be on Tuesday April 30:
https://www.bioconductor.org/developers/release-schedule/
Over the next weeks we'll announce key dates on the on bioc-devel@r-project.org
mailing list. Thanks in advance for cleaning up packages and getting those last
minut
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