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Re: [Bioc-devel] as.character method for GenomicRanges?
It would be nice to have a single function call that would hide these
details. It could probably be made more efficient also by avoiding multiple
matching, unnecessary revmap lists, etc. tableAsGRanges() is not a good
name but it conveys what I mean (does that make it actually good?).
On Mon, Apr 27, 2015 at 12:23 PM, Hervé Pagès hpa...@fredhutch.org wrote:
On 04/24/2015 11:41 AM, Michael Lawrence wrote:
Taking this a bit off topic but it would be nice if we could get the
GRanges equivalent of as.data.frame(table(x)), i.e., unique(x) with a
count mcol. Should be easy to support but what should the API be like?
This was actually the motivating use case for introducing
findMatches/countMatches a couple of years ago:
ux - unique(x)
mcols(ux)$Freq - countMatches(ux, x)
Don't know what a good API would be to make this even more
straightforward though. Maybe via some extra argument to unique()
e.g. 'with.freq'? This is kind of similar to the 'with.revmap'
argument of reduce(). Note that unique() could also support the
'with.revmap' arg. Once it does, the 'with.freq' arg can also
be implemented by just calling elementLengths() on the revmap
metadata column.
H.
On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
On 04/24/2015 10:18 AM, Michael Lawrence wrote:
It is a great idea, but I'm not sure I would use it to implement
table(). Allocating those strings will be costly. Don't we
already have
the 4-way int hash? Of course, my intuition might be completely
off here.
It does use the 4-way int hash internally. as.character() is only used
at the very-end to stick the names on the returned table object.
H.
On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès
hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org
wrote:
Hi Pete,
Excellent idea. That will make things like table() work
out-of-the-box
on GenomicRanges objects. I'll add that.
Thanks,
H.
On 04/24/2015 09:43 AM, Peter Haverty wrote:
Would people be interested in having this:
setMethod(as.character, GenomicRanges,
function(x) {
paste0(seqnames(x), :, start(x), -,
end(x))
})
?
I find myself doing that a lot to make unique names or
for
output that
goes to collaborators. I suppose we might want to tack
on the
strand if it
isn't *. I have some code for going the other
direction too,
if there is
interest.
Pete
Peter M. Haverty, Ph.D.
Genentech, Inc.
phave...@gene.com mailto:phave...@gene.com
mailto:phave...@gene.com mailto:phave...@gene.com
[[alternative HTML version deleted]]
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org
Phone: (206) 667-5791 tel:%28206%29%20667-5791
tel:%28206%29%20667-5791
Fax: (206) 667-1319 tel:%28206%29%20667-1319
tel:%28206%29%20667-1319
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org mailto:hpa...@fredhutch.org
Phone: (206) 667-5791 tel:%28206%29%20667-5791
Fax: (206) 667-1319 tel:%28206%29%20667-1319
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave.
Re: [Bioc-devel] as.character method for GenomicRanges?
On 04/27/2015 02:15 PM, Michael Lawrence wrote:
It would be nice to have a single function call that would hide these
details. It could probably be made more efficient also by avoiding
multiple matching, unnecessary revmap lists, etc. tableAsGRanges() is
not a good name but it conveys what I mean (does that make it actually
good?).
There is nothing specific to GRanges here. We're just reporting the
frequency of unique elements in a metadata column so this belongs to
the extended Vector API in the same way that findMatches/countMatches
do.
H.
On Mon, Apr 27, 2015 at 12:23 PM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
On 04/24/2015 11:41 AM, Michael Lawrence wrote:
Taking this a bit off topic but it would be nice if we could get the
GRanges equivalent of as.data.frame(table(x)), i.e., unique(x)
with a
count mcol. Should be easy to support but what should the API be
like?
This was actually the motivating use case for introducing
findMatches/countMatches a couple of years ago:
ux - unique(x)
mcols(ux)$Freq - countMatches(ux, x)
Don't know what a good API would be to make this even more
straightforward though. Maybe via some extra argument to unique()
e.g. 'with.freq'? This is kind of similar to the 'with.revmap'
argument of reduce(). Note that unique() could also support the
'with.revmap' arg. Once it does, the 'with.freq' arg can also
be implemented by just calling elementLengths() on the revmap
metadata column.
H.
On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès
hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org wrote:
On 04/24/2015 10:18 AM, Michael Lawrence wrote:
It is a great idea, but I'm not sure I would use it to
implement
table(). Allocating those strings will be costly. Don't we
already have
the 4-way int hash? Of course, my intuition might be
completely
off here.
It does use the 4-way int hash internally. as.character()
is only used
at the very-end to stick the names on the returned table
object.
H.
On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès
hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
Hi Pete,
Excellent idea. That will make things like table()
work
out-of-the-box
on GenomicRanges objects. I'll add that.
Thanks,
H.
On 04/24/2015 09:43 AM, Peter Haverty wrote:
Would people be interested in having this:
setMethod(as.character, GenomicRanges,
function(x) {
paste0(seqnames(x), :,
start(x), -,
end(x))
})
?
I find myself doing that a lot to make unique
names or for
output that
goes to collaborators. I suppose we might
want to tack
on the
strand if it
isn't *. I have some code for going the other
direction too,
if there is
interest.
Pete
Peter M. Haverty, Ph.D.
Genentech, Inc.
phave...@gene.com mailto:phave...@gene.com
mailto:phave...@gene.com mailto:phave...@gene.com
mailto:phave...@gene.com mailto:phave...@gene.com
mailto:phave...@gene.com mailto:phave...@gene.com
[[alternative HTML version deleted]]
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[Bioc-devel] biocUpgrade Wrongly Infers R Version
I can't upgrade BiocInstaller : root@bioinfo:/home/dario/Documents# R R version 3.2.0 (2015-04-16) -- Full of Ingredients Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. source(http://bioconductor.org/biocLite.R;) Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install biocLite(BiocUpgrade) Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0 sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.10 locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.4 loaded via a namespace (and not attached): [1] tools_3.2.0 Strangely, dario@bioinfo:~/Documents$ sudo R R version 3.1.1 (2014-07-10) -- Sock it to Me Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) dario@bioinfo:~/Documents$ which sudo R /usr/bin/sudo /usr/bin/R dario@bioinfo:~/Documents$ su root root@bioinfo:/home/dario/Documents# which R /usr/bin/R root@bioinfo:/home/dario/Documents# R R version 3.2.0 (2015-04-16) -- Full of Ingredients Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) Also, why does GO.db not appear in the build and check reports ? http://www.bioconductor.org/checkResults/release/bioc-LATEST/ -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Biobase: Imports repeats Depends
Hi Henrik, I know it's not necessary and I know that the WRE manual and 'R CMD check' don't like this but I like to list in Imports what I import and to list in Depends what I want to see attached to the search() path. For the same reason that I like to explicitly export the generic functions that I define in my packages even if exporting the methods defined on these generics is enough (because it has the side effect to automatically export the generic). More generally it's about expressing intentions directly versus expressing them in an indirect manner (e.g. by relying on side effects). I think the latter is wrong. Hope that makes sense. Cheers, H. On 04/25/2015 01:12 PM, Henrik Bengtsson wrote: It seems unnecessary that BiocGenerics have the same package under Imports as under Depends. The former can be dropped. packageDescription(BiocGenerics) Package: BiocGenerics Title: S4 generic functions for Bioconductor Description: S4 generic functions needed by many Bioconductor packages. Version: 0.14.0 Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer maintai...@bioconductor.org biocViews: Infrastructure Depends: methods, utils, graphics, stats, parallel Imports: methods, utils, graphics, stats, parallel Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit License: Artistic-2.0 Collate: S3-classes-as-S4-classes.R normarg-utils.R update-utils.R . NeedsCompilation: no Packaged: 2015-04-17 03:42:27 UTC; biocbuild Built: R 3.3.0; ; 2015-04-25 20:08:25 UTC; windows /Henrik ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioc package pages: List also BugReports for a package?
- Original Message - From: Henrik Bengtsson henrik.bengts...@ucsf.edu To: bioC-devel bioc-de...@stat.math.ethz.ch Sent: Sunday, April 26, 2015 7:14:20 PM Subject: [Bioc-devel] Bioc package pages: List also BugReports for a package? For affxparser, we've got the following in DESCRIPTION: URL: https://github.com/HenrikBengtsson/affxparser BugReports: https://github.com/HenrikBengtsson/affxparser/issues But t's only the URL field that is listed on the package page(s): http://www.bioconductor.org/packages/release/bioc/html/affxparser.html http://www.bioconductor.org/packages/devel/bioc/html/affxparser.html May I suggest to also have BugReports listed on package pages? Done (only added if the package DESCRIPTION contains a BugReports field). Dan Thanks, Henrik ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] seqnames as a candidate for BiocGenerics
Probably because that would mean genomeIntervals depending on IRanges. Because GenomeInfoDb needs CompressedList. On Mon, Apr 27, 2015 at 11:14 AM, Hervé Pagès hpa...@fredhutch.org wrote: Hi Nico, On 04/26/2015 09:58 AM, Nicolas Delhomme wrote: Hej Hervé (I guess)! Could it be possible to move the generic from seqnames and seqnames- from GenomeInfoDb to BiocGenerics? I would then deprecate the seq_name and seq_name- functions of the genomeIntervals package and import them in the easyRNASeq package. I guess I could. However I want to make it clear that a generic function doesn't have to go to BiocGenerics before it can be shared across packages. There are situations where this kind of move actually helps to resolve conflicts but it doesn't seem to be the case here. Any reason why you can't just import GenomeInfoDb? This is what all the packages that need the seqnames and seqnames- generics currently do. Moving these generics to BiocGenerics will likely break many of them. Thanks, H. Cheers, Nico --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] seqnames as a candidate for BiocGenerics
Hej Michael and Hervé! Importing from GenomeInfoDb is what I do at the moment. I will have to check more extensively - adding more unit tests - but it seems to work so far, without depending on IRanges - thanks Michael I'll keep that in mind while testing. I just had the understanding that if many packages needed the same generic, such generics were candidates for being ported to BiocGenerics simply because it would be more consistent to have them in BiocGenerics; that's all. But I also understand the cons and importing from GenomeInfoDb is certainly the path of least resistance ;-) Thanks for the feedback, I'll come back to you if the point raised by Michael occurs. Cheers, Nico --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- On 27 Apr 2015, at 20:22, Michael Lawrence lawrence.mich...@gene.com wrote: Probably because that would mean genomeIntervals depending on IRanges. Because GenomeInfoDb needs CompressedList. On Mon, Apr 27, 2015 at 11:14 AM, Hervé Pagès hpa...@fredhutch.org wrote: Hi Nico, On 04/26/2015 09:58 AM, Nicolas Delhomme wrote: Hej Hervé (I guess)! Could it be possible to move the generic from seqnames and seqnames- from GenomeInfoDb to BiocGenerics? I would then deprecate the seq_name and seq_name- functions of the genomeIntervals package and import them in the easyRNASeq package. I guess I could. However I want to make it clear that a generic function doesn't have to go to BiocGenerics before it can be shared across packages. There are situations where this kind of move actually helps to resolve conflicts but it doesn't seem to be the case here. Any reason why you can't just import GenomeInfoDb? This is what all the packages that need the seqnames and seqnames- generics currently do. Moving these generics to BiocGenerics will likely break many of them. Thanks, H. Cheers, Nico --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] as.character method for GenomicRanges?
On 04/24/2015 11:41 AM, Michael Lawrence wrote:
Taking this a bit off topic but it would be nice if we could get the
GRanges equivalent of as.data.frame(table(x)), i.e., unique(x) with a
count mcol. Should be easy to support but what should the API be like?
This was actually the motivating use case for introducing
findMatches/countMatches a couple of years ago:
ux - unique(x)
mcols(ux)$Freq - countMatches(ux, x)
Don't know what a good API would be to make this even more
straightforward though. Maybe via some extra argument to unique()
e.g. 'with.freq'? This is kind of similar to the 'with.revmap'
argument of reduce(). Note that unique() could also support the
'with.revmap' arg. Once it does, the 'with.freq' arg can also
be implemented by just calling elementLengths() on the revmap
metadata column.
H.
On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
On 04/24/2015 10:18 AM, Michael Lawrence wrote:
It is a great idea, but I'm not sure I would use it to implement
table(). Allocating those strings will be costly. Don't we
already have
the 4-way int hash? Of course, my intuition might be completely
off here.
It does use the 4-way int hash internally. as.character() is only used
at the very-end to stick the names on the returned table object.
H.
On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès
hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org wrote:
Hi Pete,
Excellent idea. That will make things like table() work
out-of-the-box
on GenomicRanges objects. I'll add that.
Thanks,
H.
On 04/24/2015 09:43 AM, Peter Haverty wrote:
Would people be interested in having this:
setMethod(as.character, GenomicRanges,
function(x) {
paste0(seqnames(x), :, start(x), -,
end(x))
})
?
I find myself doing that a lot to make unique names or for
output that
goes to collaborators. I suppose we might want to tack
on the
strand if it
isn't *. I have some code for going the other
direction too,
if there is
interest.
Pete
Peter M. Haverty, Ph.D.
Genentech, Inc.
phave...@gene.com mailto:phave...@gene.com
mailto:phave...@gene.com mailto:phave...@gene.com
[[alternative HTML version deleted]]
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org
Phone: (206) 667-5791 tel:%28206%29%20667-5791
tel:%28206%29%20667-5791
Fax: (206) 667-1319 tel:%28206%29%20667-1319
tel:%28206%29%20667-1319
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org mailto:hpa...@fredhutch.org
Phone: (206) 667-5791 tel:%28206%29%20667-5791
Fax: (206) 667-1319 tel:%28206%29%20667-1319
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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