- Original Message -
> From: "Karl Stamm"
> To: bioc-devel@r-project.org
> Sent: Monday, September 29, 2014 10:04:40 PM
> Subject: [Bioc-devel] new package build problems
>
> I'm trying to put together a new package submission, "rgsepd", and
> I've ran
> into an error I can't figure out
I'm trying to put together a new package submission, "rgsepd", and I've ran
into an error I can't figure out. Hoping to talk with someone with more
experience on the bioconductor build system.
The build report is here
http://bioconductor.org/spb_reports/rgsepd_0.99.2_buildreport_20140929213816.htm
I admit negligence in not document this. But if you look at VRanges, you
can see how we set a method for "extraColumnSlotNames" returns a character
vector of slot names to tell GenomicRanges which slots should be treated as
columns (there is also an example in the previous email). These are then
ha
Based on Chuck's email I realize I did not understand Michael's answer at
all.
On Mon, Sep 29, 2014 at 7:44 PM, Charles Berry wrote:
> Michael Lawrence gene.com> writes:
>
> >
> > This comes down to an inheritance vs. composition decision, but I hope
> > everyone is aware of the extraColumnSlot
Michael Lawrence gene.com> writes:
>
> This comes down to an inheritance vs. composition decision, but I hope
> everyone is aware of the extraColumnSlots mechanism in GRanges that makes
> it easy to add additional "column-shaped" slots to a subclass of GRanges.
Where is it documented, please?
Martin, I think Time explained it pretty well. All I am saying is that it
would be convenient to have a class which represents that another class can
be treated as a GRanges.
In bsseq I have one such class: BSseqTstat. I used to also construct the
BSseq class like this, but since it is essential
Hi Kasper,
The reduceBy* functions were intended to combine data across ranges or
files. If we have 10 ranges and 3 files you can think of it as a 10 x 3
grid where we'll have 30 queries and therefore 30 pieces of information
that can be combined across different dimensions.
The request to '
I wrote it, because it might be clearer to see it as code:
###
=
### DelegatingGenomicRanges objects
###
-
###
### Virtual class that delegates GenomicRan
Hi Michel,
In BiocParallel 0.99.24 .convertToSimpleError() now checks for NULL and
converts to NA_character_.
I'm testing with BatchJobs 1.4, BiocParallel 0.99.24 and SLURM. I'm
still not getting an informative error message:
xx <- bplapply(1:2, FUN)
SubmitJobs |++
This comes down to an inheritance vs. composition decision, but I hope
everyone is aware of the extraColumnSlots mechanism in GRanges that makes
it easy to add additional "column-shaped" slots to a subclass of GRanges.
It may be that hasGRanges could take a similar approach, except support
composit
Just to support Kasper's proposal, I see this as being broadly useful.
It's really common to be dealing with an object (say, a
SummarizedExperiment-derived doohickey, or a transcriptDb-looking whatzit,
or "bumps", or "dmrcoutput") that has metadata which "looks like" a
GRanges. More often than n
Unfortunately this approach is limited to apps where the UI of the app is
defined in R code. For more involved GUI development it is much preferred to
write the HTML yourself and for this to work, there need to be a server.R file.
I don’t think we should have recommendations that limits the deve
On 09/28/2014 07:49 PM, Kasper Daniel Hansen wrote:
3. (well, this is GenomicRanges) It seems like GenomicFiles has a lot of
similarities with SummarizedExperiment. I have a lot of use cases for a
simple class which has a single GRanges slot, and then support stuff like
granges(), start(), end()
- Original Message -
> From: "Thomas Dybdal Pedersen"
> To: bioc-devel@r-project.org
> Sent: Monday, September 29, 2014 12:49:16 PM
> Subject: [Bioc-devel] Guidelines for shiny packages
>
> Hi All
>
> I’m in the process of getting package submitted to Bioconductor. The
> package is a p
Hi All
I’m in the process of getting package submitted to Bioconductor. The package is
a pure shiny package and this has led to some - especially one question. For
those not familiar with shiny apps, the code that makes these work resides in
their own .R files outside of the R directory in a pa
- Original Message -
> From: "Wolfgang Huber"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Monday, September 29, 2014 12:35:18 PM
> Subject: Re: [Bioc-devel] Workflows
>
> Dear Dan
>
> Thanks. What is the recommended procedure for people wanting to run
> the workflow o
Dear Dan
Thanks. What is the recommended procedure for people wanting to run the
workflow on their own computer? (E.g. for teaching).
Or even to prevent them from doing odd things like using the wrong versions of
R and packages?
Best wishes
Wolfgang
Il giorno Sep 29, 2014, alle ore 21:32
- Original Message -
> From: "Wolfgang Huber"
> To: bioc-devel@r-project.org
> Sent: Monday, September 29, 2014 12:24:54 PM
> Subject: [Bioc-devel] Workflows
>
>
> Sorry if I have overlooked something… referring to
> http://www.bioconductor.org/developers/how-to/workflows Is there a
>
Hi Florian,
True. These restrictions don't make much sense these days anymore!
Some of them are gone in the devel version of BSgenome. The
BSgenomeForge vignette in devel now says:
The sequence data must be in a single twoBit file (e.g. musFur1.2bit)
or in a collection of FASTA files (possib
Sorry if I have overlooked something… referring to
http://www.bioconductor.org/developers/how-to/workflows Is there a standardized
way to manage
- dependencies
- versions
In principle, these could be automagically computed (?), but would still have
to be exposed to workflow users using an afaI
Reminder, this is tomorrow.
Dan
- Forwarded Message -
From: "Dan Tenenbaum"
To: "bioc-devel"
Sent: Wednesday, September 17, 2014 1:35:39 PM
Subject: [Bioc-devel] hedgehog Subversion server upgrade Tuesday 9/30
Hello Bioconductor developers,
On Tuesday 9/30 at 8:00 AM (Seattle time), t
On Mon, Sep 29, 2014 at 9:09 AM, Kasper Daniel Hansen
wrote:
> I don't fully understand "the use case for reducing by range is when the
> entire dataset won't fit into memory". The basic assumption of these
> functions (as far as I can see) is that the output data fits in memory.
> What may not f
I don't fully understand "the use case for reducing by range is when the
entire dataset won't fit into memory". The basic assumption of these
functions (as far as I can see) is that the output data fits in memory.
What may not fit in memory is various earlier "iterations" of the data.
For example,
Thanks for checking it out and benchmarking. We should be more clear
in the docs that the use case for reducing by range is when the entire
dataset won't fit into memory. Also, we had some discussion and
Valerie had written up methods for packing up the ranges supplied by
the user into a better for
Hi all,
I was wondering whether some of the rather arbitrary restrictions on input
files for the process of forging as new Bsgenome package could be liftet. In
particular:
Why do we need all chromosomes in individual files? Couldn�t the function be
smart enough to just extract the relevant bits
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