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, especially when they try to access the man page for
normalize(). But if we are happy with that, then I don't really see
the need to put normalize() in BiocGenerics.
Cheers,
H.
On 02/20/2013 11:52 AM, Robert Gentleman wrote:
my 2c worth
On Wed, Feb 20, 2013 at 10:45 AM, Hervé Pagès hpa...@fhcrc.org
On 02/20/2013 01:02 PM, Hervé Pagès wrote:
...
Furthermore, the good citizens that modify their package to use the
normalize() in BiocGenerics will be in a situation worth than before
because, from an end user point of view, their normalize() function
(which is now a method attached
Jirka
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Hi Laurent, Robert, and others,
On 02/20/2013 01:33 PM, Laurent Gautier wrote:
On 2013-02-20 22:02, Hervé Pagès wrote:
Hi Robert,
Nice to hear from you!
I'm just a little bit worried that if we put normalize() in
BiocGenerics without at the same time have a take it or leave it
policy
0
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-devel
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2.15.2 Patched (2012-11-12 r61105)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
other attached packages:
[1] IRanges_1.16.6 BiocGenerics_0.4.0 devtools_1.1
-steve
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Julian
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for unlisting, but for many other
operations.
HTH,
H.
Best wishes
Julian
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,
Stephanie
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version
rather than
from the current Bioconductor release?
The page at http://bioconductor.org/install/ does _not_ mention this
important
fact! Could somebody please fix this?
Simon
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) and everybody knows
that this means less features, more bugs, a more restrictive
license, more memory requirements, etc... ;-)
H.
On 06/19/2013 10:50 PM, Martin Morgan wrote:
On 06/19/2013 09:15 PM, Hervé Pagès wrote:
Hi Martin,
On 06/19/2013 05:21 PM, Martin Morgan wrote:
On 06/19/2013 03:01 PM
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.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
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MA 01605
On 7/23/13 5:35 PM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi,
This fails in Bioc-devel only and the following fix seems to address
the problem:
hpages@thinkpad:~/svn
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some suggestions...
On Tue, Sep 17, 2013 at 10:58 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
For sorting the chromosome names in natural order, you can use
the makeSeqnameIds() helper function in GenomicRanges:
seqlevels(gr) - seqlevels(gr)[makeSeqnameIds
, Michael Lawrence
lawrence.mich...@gene.com wrote:
On Mon, May 20, 2013 at 10:36 PM, Hervé Pagès hpa...@fhcrc.org wrote:
Michael,
On 05/20/2013 08:44 PM, Michael Lawrence wrote:
On Mon, May 20, 2013 at 4:13 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi
, that's great.
Would it make sense to have a sort or sortSeqlevels method for Seqinfo
and then a sortSeqlevels,ANY method that just does seqinfo(x) -
sort(seqinfo(x))?
Michael
On Tue, Sep 17, 2013 at 12:56 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 09/17/2013 10:58 AM
On 09/17/2013 10:58 AM, Hervé Pagès wrote:
For sorting the chromosome names in natural order, you can use
the makeSeqnameIds() helper function in GenomicRanges:
seqlevels(gr) - seqlevels(gr)[makeSeqnameIds(seqlevels(gr))]
I meant:
seqlevels(gr) - seqlevels(gr)[order(makeSeqnameIds
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in the future we could have something
like fixSeqlevels() for doing both: sorting and renaming.
Cheers,
H.
Best,
Kasper
On Tue, Sep 17, 2013 at 4:22 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
OK I just made sortSeqlevels() a generic with a method for character
for implementing
seqlevels in here in the 1st place). Now I could make it more
convenient here and break consistency with how it is used elsewhere, but
what do people prefer?
Consistent or convenient?
Marc
On 09/18/2013 10:40 AM, Hervé Pagès wrote:
Hi Marc,
Wouldn't it make sense to just
he knows, nor judge all he sees.*
*
*
Benjamin Franklin, Poor Richard's
Almanackhttp://archive.org/details/poorrichardsalma00franrich
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stats4_3.0.2 stringr_0.6.2
[8] tools_3.0.2whisker_0.3-2
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tools_3.0.2
[11] whisker_0.3-2 zlibbioc_1.8.0
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with the behavior of ordinary vectors.
The only difference with Lists is that there is a partitioning, which
seems unrelated to naming.
Michael
On Tue, Oct 29, 2013 at 3:40 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Thomas,
For the same reasons that you cannot
On 10/30/2013 07:55 AM, Michael Lawrence wrote:
On Tue, Oct 29, 2013 at 5:55 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
In Bioc 2.13, subsetting was a mess. In particular, handling of
list-like subscripts was rather unpredictable. It would work
On 10/30/2013 10:07 AM, Michael Lawrence wrote:
On Wed, Oct 30, 2013 at 8:37 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 10/30/2013 07:55 AM, Michael Lawrence wrote:
On Tue, Oct 29, 2013 at 5:55 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa
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On 11/06/2013 11:29 AM, Michael Lawrence wrote:
Great, thanks for updating. I legitimately wanted to use %in%, not %over%.
Great to hear you have a use case for %in% (with the new behavior). So
I'm not the only one ;-)
H.
Michael
On Wed, Nov 6, 2013 at 10:59 AM, Hervé Pagès hpa
called here. I'll
change this.
H.
Thanks,
Michael
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the externalVector package?
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that use
it? Would be interesting to have a look at them.
H.
Michael
On Sun, Dec 8, 2013 at 11:39 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
The OnDiskXRaw virtual class (if this is what you're referring to)
is still a very early work-in-progress
for mmap
and HDF5 for example. They don't necessarily have to be implemented in
XVector.
H.
Kasper
On Mon, Dec 9, 2013 at 1:46 PM, Michael Lawrence
lawrence.mich...@gene.com mailto:lawrence.mich...@gene.com wrote:
On Mon, Dec 9, 2013 at 9:30 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa
Hi developpers,
Just wanted to announce the new GenomicAlignments package in BioC
devel. It's a split from the GenomicRanges package that contains:
- The GAlignments/GAlignmentPairs/GAlignmentsList classes
and the readGAlignment*() functions.
- The CIGAR low-level utilities and the
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))]
But this is still better:
sort(gr, ignore.strand=TRUE)
Sound like a good thing?
Michael
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for someone to speak up.
H.
Michael
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(internal helper normalizeSingleBracketSubscript actually
does that). However I would still recommend you use the latter in
your package so it will take advantage of optimizations that might
happen in the future.
H.
On Fri, Dec 13, 2013 at 6:19 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org
zlibbioc_1.9.0
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] On Behalf Of Hervé Pagès
Sent: Tuesday, 17 December 2013 8:27 p.m.
To: Kasper Daniel Hansen
Cc: Michael Lawrence; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] ordering GenomicRanges without regard for strand
OK. Let's go for unstrand() too. Will add this in the next few days.
H.
On 12/12
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, an odd y in devel, with y bump (and z reset to 0) at each
new release. Feedback welcome.
Please let me know if you have questions or concerns about this.
Cheers,
H.
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On 01/22/2014 03:02 PM, Michael Lawrence wrote:
On Wed, Jan 22, 2014 at 1:29 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
On 01/12/2014 05:16 AM, Michael Lawrence wrote:
Hi,
It may be time to deprecate the seq*apply family
On 01/22/2014 08:15 PM, Michael Lawrence wrote:
Sounds good. But who is she?
we would, she should, she would, we should... that's it! we should...
that's what I meant :-b
H.
On Wed, Jan 22, 2014 at 3:48 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 01/22/2014 03
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...)
Cheers,
H.
coverage() is fast and beautiful. Thanks!
/Jesper
On Wed, Feb 19, 2014 at 9:21 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Jesper,
On 02/19/2014 08:44 AM, Michael Lawrence wrote:
On Wed, Feb 19, 2014 at 8:39 AM, Jesper Gådin
On 02/20/2014 02:55 PM, Martin Morgan wrote:
On 02/20/2014 02:32 PM, Hervé Pagès wrote:
Hi Jesper,
On 02/20/2014 02:13 PM, Jesper Gådin wrote:
Very true that it is quite difficult to find the documentation when one
is not aware of its existence :P
Yeah, this has been a source
the
examples below. If the function is not a generic (no S4 methods
are defined for it), the help reverts to documentation on the
function name.
Thanks,
H.
On Fri, Feb 21, 2014 at 11:17 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Gabriel,
On 02/20/2014
, ...) to find out what particular
method was being called (I needed to see the code).
Thanks,
H.
On 02/22/2014 05:59 AM, Michael Lawrence wrote:
Translated it into a patch against R, submitted here:
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15680
On Fri, Feb 21, 2014 at 2:53 PM, Hervé Pagès
‘c’ and signature ‘x = IRanges,
recursive = logical’
Thanks again for working on this.
H.
Michael
On Sat, Feb 22, 2014 at 12:26 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Thanks Michael.
Do you think it would be sensible to offer a similar fix
/listinfo/bioc-devel
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be by regex
and package name. Still a work in progress.
Valerie
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On 03/11/2014 02:52 PM, Hervé Pagès wrote:
On 03/11/2014 09:57 AM, Valerie Obenchain wrote:
Hi Herve,
On 03/10/2014 10:31 PM, Hervé Pagès wrote:
Hi Val,
I think it would help understand the motivations behind this proposal
if you could give an example of a method where the user cannot supply
Hi Val,
On 03/11/2014 08:57 PM, Valerie Obenchain wrote:
Hi,
On 03/11/14 15:33, Hervé Pagès wrote:
On 03/11/2014 02:52 PM, Hervé Pagès wrote:
On 03/11/2014 09:57 AM, Valerie Obenchain wrote:
Hi Herve,
On 03/10/2014 10:31 PM, Hervé Pagès wrote:
Hi Val,
I think it would help understand
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
[...]
Following that logic names(se1) also probably return colnames(se1).
/\
should
H.
H.
On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey
st...@channing.harvard.eduwrote
Hi Martin,
On 03/21/2014 01:45 PM, Martin Morgan wrote:
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little
surprising;
I learned it from restrictToSNV.
This is inherited from
by
sealed=TRUE, but that did not work either. Any ideas are
gratefully
appreciated!
Thanks a lot,
Ulrich
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element, but I wanted the line above to
do that.
Michael
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() (they're just fast equivalent to 'mapply(head, x, n)' and
'mapply(tail, x, n))', or...?
Thanks,
H.
Michael
On Tue, Apr 1, 2014 at 12:06 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 04/01/2014 10:17 AM, Ryan wrote:
That won't work if any vector has fewer than
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Added in IRanges 1.21.41.
H.
On 04/01/2014 06:15 PM, Michael Lawrence wrote:
I like phead/ptail. I was going to write them, so thanks for taking care
of it!
Michael
On Tue, Apr 1, 2014 at 3:24 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 04/01/2014 02:43 PM
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Phone: (206) 667-5791
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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...@fhcrc.org
Phone: (206
with BiocGenerics around, it's hard to avoid this kind of clash.
H.
Best wishes,
Laurent
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Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446
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.
On Wed, Apr 16, 2014 at 12:59 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Sean
[hope you don't mind if I cc Bioc-devel]
On 04/15/2014 11:47 PM, Maintainer wrote:
Hi The Bioconductor Dev Team,
A new package called BSgenome.Hsapiens.NCBI.GRCh38
version deleted]]
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,
some turbulences on the build report are to be expected. I'll keep a
close eye on that and fix the packages affected by this split.
Thanks,
H.
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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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...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319 %28206%29
://stat.ethz.ch/mailman/listinfo/bioc-devel
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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...@fhcrc.org
Phone: (206) 667-5791
Fax:(206
versioning
http://bioconductor.org/developers/how-to/version-numbering/
and the Bioc-style approach to release that we as developers can act
on to enhance reproducibility. What other best pract
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson
On Tue, Apr 29, 2014 at 11:24 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
I noticed this difference between DataFrame vs data.frame when doing
rbind():
rbind(data.frame(aa=NA), data.frame(aa=1:2))
aa
1 NA
2 1
3
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Fred
]]
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Program in Computational Biology
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle
.
to work?
hint: it does not
-Original Message-
From: bioc-devel-boun...@r-project.org
[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès
Sent: Monday, May 05, 2014 1:28 PM
To: Kasper Daniel Hansen; Michael Lawrence
Cc: Johnston, Jeffrey; ttri...@usc.edu; bioc-devel
this.
Cheers,
H.
to work?
hint: it does not
-Original Message-
From: bioc-devel-boun...@r-project.org
[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès
Sent: Monday, May 05, 2014 1:28 PM
To: Kasper Daniel Hansen; Michael Lawrence
.
metadata(ans) - metadata(x)
names(ans) - names(x)
mcols(ans) - mcols(x)
ans
}
)
###
Kind regards,
Sebastian
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in using
GenomeData/GenomeDataList over GRanges/GRangesList.
Thanks,
H.
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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...@fhcrc.org
Phone: (206
, 2014 at 3:32 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi,
I'd like to deprecate the GenomeData and GenomeDataList classes defined
in the BSgenome package. If you've never heard about these containers,
you can stop reading here.
I was able to find only 2
?
Thanks,
H.
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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...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
) is
ever released. The memory leak is minor if the sequence passed via
'object' has no masks but can be important if there are masks and
if the masks are made of hundreds of thousands of ranges.
Thanks,
H.
On Fri, May 9, 2014 at 4:07 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org
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