On 06/11/2015 11:50 AM, Hervé Pagès wrote:
Hi Stephanie,
On 06/11/2015 11:33 AM, Gabe Becker wrote:
Stephanie,
As far as I know, it is so that package versions are unique to specific
releases of bioconductor. This has the benefits of
1. providing assurances that that particular version
...@gene.com wrote:
Maybe this could eventually support setting the seqinfo with:
genome(gr) - hg19
Or is that being too clever?
On Thu, Jun 4, 2015 at 4:28 PM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
Hi,
FWIW I started to work
On 06/05/2015 11:43 AM, Michael Lawrence wrote:
On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès hpa...@fredhutch.org wrote:
I also think that we're heading towards something like that.
So genome(gr) - hg19 would:
(a) Add any missing information to the seqinfo.
(b) Sort the seqlevels
...@gene.com
wrote:
On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès hpa...@fredhutch.org
wrote:
I also think that we're heading towards something like that.
So genome(gr) - hg19 would:
(a) Add any missing information to the seqinfo.
(b) Sort the seqlevels in canonical order.
(c) Change
is the grammar of science.
Karl Pearson http://en.wikipedia.org/wiki/The_Grammar_of_Science
On Fri, Jun 5, 2015 at 1:36 PM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
On 06/05/2015 01:19 PM, Michael Lawrence wrote:
To support the multi-genome case, one could set
(Which
it sometimes would do.
gr - fixSeqInfo(gr, hg19)
instead?
~G
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Thanks Martin for looking into this. H.
On 05/13/2015 03:57 AM, Martin Maechler wrote:
Hervé Pagès hpa...@fredhutch.org
on Tue, 12 May 2015 15:18:42 -0700 writes:
Hi,
The man page for new() suggests that if 'a' is an object with slots
slot1 and slot2 and C is a class that extends
base
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though...
H.
On 05/12/2015 03:22 PM, Michael Lawrence wrote:
It's more general than SummarizedExperiment. I think people would
appreciate a simple way to load the core, without having to remember,
for example, that VCF reading is in VariantAnnotation.
On Mon, May 11, 2015 at 9:51 PM, Hervé Pagès
Hi Michael,
I finally got to fix this in Biostrings 2.36.1 (release) and 2.37.2
(devel). Both should become available via biocLite() on Friday around
11am (Seattle time). Thanks for your patience.
Cheers,
H.
On 04/30/2015 10:50 AM, Hervé Pagès wrote:
Hi Michael,
Thanks for the reminder. I
.
But of course, it may be interesting to hear other programmeR's
feedback on this.
Martin
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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
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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
. Haverty, Ph.D.
Genentech, Inc.
phave...@gene.com mailto:phave...@gene.com
On Fri, Apr 24, 2015 at 10:50 AM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
On 04/24/2015 10:21 AM, Michael Lawrence wrote:
Sorry, one more concern, if you're thinking of using
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 wrote:
Hi Pete,
Excellent idea. That will make things like table() work out-of-the-box
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Hi,
On 04/17/2015 09:42 AM, Hervé Pagès wrote:
Hi,
I think we should just expand the Rle internally. That will produce
a numeric vector of the length of the GRanges i.e. it will be the
same size as the start and end components of the GRanges object itself.
No big deal at all.
I'll make
On 04/17/2015 10:00 AM, Michael Lawrence wrote:
Is that the case here? He has an Rle as an mcol in the GRanges, so in
general expanding it will not align with the other components.
Not sure what you mean. Can you give an example?
H.
On Fri, Apr 17, 2015 at 9:42 AM, Hervé Pagès hpa
On 04/17/2015 08:24 AM, Martin Maechler wrote:
Martin Maechler maech...@lynne.stat.math.ethz.ch
on Fri, 17 Apr 2015 15:49:35 +0200 writes:
Hervé Pagès hpa...@fredhutch.org
on Mon, 13 Apr 2015 23:36:14 -0700 writes:
On 04/13/2015 11:32 PM, Martin Maechler wrote
}}
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Hi Martin,
On 04/17/2015 06:49 AM, Martin Maechler wrote:
Hervé Pagès hpa...@fredhutch.org
on Mon, 13 Apr 2015 23:36:14 -0700 writes:
On 04/13/2015 11:32 PM, Martin Maechler wrote:
Hi,
as.integer(50)
[1] 2147483647
Warning message
by injecting an arbitrary (and potentially long) list of strings.
Thanks,
H.
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that NAs where introduced by coercion is important.
Yes.
The message is less a problem than the bug, but I agree we
should try to improve it.
Sounds good. Thanks Martin,
H.
Martin
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with:
as.integer(-50)
[1] NA
Warning message:
NAs introduced by coercion
In the case of as.integer(-50), it's not really that the
conversion was inaccurate, it's a little bit worse than that. And
knowing that NAs where introduced by coercion is important.
Thanks,
H.
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and fetchChromLengthsFromEnsemblPlants in
GenomicFeatures, as I find these methods quite useful to retrieve chromosome lengths.
best, jo
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the dist class.
H.
On Wed, Apr 1, 2015 at 4:29 PM, Martin Morgan mtmor...@fredhutch.org
mailto:mtmor...@fredhutch.org wrote:
On 04/01/2015 03:52 PM, Hervé Pagès wrote:
Hi,
In the same way that we avoid having 2 packages define the same
S4 generic function
So I went ahead and did BSgenome.Btaurus.UCSC.bosTau8. It should
become available via biocLite() in the next couple of hours (in
BioC devel only).
H.
On 03/26/2015 12:54 AM, Hervé Pagès wrote:
Hi Byungkuk,
On 03/25/2015 10:17 PM, Byungkuk Min wrote:
Dear Dr.Pages,
I've been trying to build
On 03/16/2015 07:36 PM, Valerie Obenchain wrote:
On 03/16/2015 05:31 PM, Hervé Pagès wrote:
On 03/16/2015 04:06 PM, Michael Lawrence wrote:
On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo robert.cast...@upf.edu
mailto:robert.cast...@upf.edu wrote:
+1 IMO BioC could adopt the zero
On Mon, Mar 16, 2015 at 3:38 PM, Hervé Pagès
hpa...@fredhutch.org mailto:hpa...@fredhutch.org
mailto:hpa...@fredhutch.org mailto:hpa...@fredhutch.org wrote:
On 03/16/2015 09:22 AM, Michael Lawrence wrote:
Yes, I think it would make sense for the Xtra package
in having core packages use exactly the
same representation; I don't have any opinion about which one is
best.
Kasper
On Mon, Mar 16, 2015 at 3:38 PM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
On 03/16/2015 09:22 AM, Michael Lawrence wrote:
Yes, I think
-devel
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Structural Biology, Department of Epidemiology Biostatistics
UT Health Science Center at San Antonio
email: liu...@uthscsa.educel: 210-784-0828
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. It makes sense since this
ensures continuous availability of the package.
Cheers,
H.
Cheers,
- Gord
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PM, Hervé Pagès wrote:
On 03/03/2015 02:28 AM, Martin Maechler wrote:
Diverted from R-help :
as it gets into musing about new R language primitives
William Dunlap wdun...@tibco.com
mailto:wdun
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On 03/02/2015 01:00 PM, Hervé Pagès wrote:
Hi,
On 03/02/2015 12:18 PM, Dénes Tóth wrote:
On 03/02/2015 04:37 PM, Martin Maechler wrote:
On 2 March 2015 at 09:09, Duncan Murdoch wrote:
| I generally recommend that people use Rcpp, which hides a lot of the
| details. It will generate your
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On 02/27/2015 03:28 PM, Martin Morgan wrote:
I noticed that we're at r99955 in svn; who will be the lucky person
making the 100,000th commit?
depends how many zeroes after the one you're gonna put on the
check... 5?
;-)
H.
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by these ranges.
H.
On 02/25/2015 01:21 PM, Hervé Pagès wrote:
Hi,
On 02/25/2015 06:37 AM, Gabe Becker wrote:
I think we need to be a little careful of trying to know the users
intentions better than they do here. Reduce is a (very) easy operation
to do on a GRanges, so if the user didn't, are we really
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that the package I developed (prebs) gives this warning:
Warning: 'readGAlignmentsFromBam' is deprecated.
What is the new function that should be used instead of
readGAlignmentsFromBam (GenomicAlignments package)? Do the changes
affect readGAlignmentPairs function, too?
Regards,
Karolis
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..., see ?`Hits-comparison` in S4Vectors).
Cheers,
H.
On Thu, Jan 15, 2015 at 11:34 AM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
Hi guys,
Indeed, the Hits object returned by findOverlaps() is not fully
sorted anymore. Now it's sorted by query hit *only
Hi,
On 01/08/2015 07:02 AM, Martin Maechler wrote:
Adding an optional argument to get (and mget) like
val - get(name, where, ..., value.if.not.found=NULL ) (*)
would be useful for many. HOWEVER, it is possible that there could be
some confusion here: (*) can give a NULL because either x
, nomatch = 0L) 0L) ?
H.
-pd
On 06 Jan 2015, at 22:02 , Hervé Pagès hpa...@fredhutch.org wrote:
Hi,
Current implementation:
setequal - function (x, y)
{
x - as.vector(x)
y - as.vector(y)
all(c(match(x, y, 0L) 0L, match(y, x, 0L) 0L))
}
First what about replacing 'match(x, y, 0L) 0L
seems to speed up things a little bit (not in a significant
way though).
Cheers,
H.
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Hi Gordon,
My guess is that it has to do with how many symbols get exported.
For example on my machine, doing library(limma) in a fresh session
takes 0.261s and triggers export of 292 symbols (as reported by
ls(..., all.names=TRUE)). Doing library(GenomicRanges) in a fresh
session takes 2.724s
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for ScalarInteger or ScalarReal. I am currently working
around this using duplicate(ScalarLogical(0)), but was quite surprised
by this behavior of ScalarLogical.
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for ScalarInteger or ScalarReal. I am currently working
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by this behavior of ScalarLogical.
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On 10/28/2014 12:42 PM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
Hi,
On 10/28/2014 08:48 AM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 11:23 AM, Kasper Daniel Hansen
value is
truncated to length 0 and no warning is issued. Makes sense to me.
Cheers,
H.
/Henrik
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Hi,
On 10/24/2014 06:58 AM, S Ellison wrote:
Also note that these warnings or errors are complaining that the
number of items to replace (left length) is not a multiple of
replacement length (right length). This suggests that when the left
length is a multiple of the right length, everything is
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: namespace:GenomicAlignments
What is the rationale for setting `drop.D.ranges` by default to FALSE?
Because last time I checked (but that was 3 or 4 years ago), that's what
Samtools pileup was doing.
Cheers,
H.
Thanks,
Leo
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package will still be able to see useful
information and that information will be placed where developers
expect it to be: in the source code itself.
My 2 cents.
Cheers,
H.
thank you for your help,
Tiphaine
From: Hervé Pagès hpa...@fhcrc.org
Sent: 14 October
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we get the warning for the edge-case where
one of the 2 Seqinfo objects is empty. In that particular case the
warning is arguably not useful so I just removed it.
H.
On Sun, Oct 12, 2014 at 11:46 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
On 10/12
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loading sequence?
thanks again!
robert.
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of the assigned genomes, we
should*
*not issue this warning.*
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to deal with gzipped fasta files these days.
Thanks,
Florian
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will hopefully
go away if you reinstall the package. Let me know if it doesn't.
Hope this helps,
H.
Best,
Jim
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Hi developers,
I recently moved SimpleList and DataFrame from IRanges to S4Vectors.
That breaks a number of packages as you can see on today's build/check
report:
http://bioconductor.org/checkResults/3.0/bioc-LATEST/
Will fix today. Sorry for the inconvenience.
Cheers,
H.
...@channing.harvard.edu
wrote:
On Tue, Sep 9, 2014 at 12:30 AM, Hervé Pagès hpa...@fhcrc.org wrote:
On 09/08/2014 06:42 PM, Michael Lawrence wrote:
Instead of printing out multiple lines of a table that is rarely of
interest, could we develop Peter's idea toward something like:
hg19:chr1 hg19
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/S4Vector stuff. My fault, not yours.
Val
On 09/09/2014 02:47 PM, Hervé Pagès wrote:
Hi Val,
On 09/09/2014 02:12 PM, Valerie Obenchain wrote:
Writing 'list' data has been fixed in 1.11.30. fyi, Herve is in the
process of moving SimpleList and DataFrame from IRanges to S4Vectors;
finished up today I
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of this.
On Mon, Sep 8, 2014 at 10:50 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Vince,
Yes it would make sense to have the show method report the genome
when genome(x) contains a unique non-NA value. I think the main
use case for having the genome defined at the sequence
On 09/08/2014 02:28 PM, Peter Hickey wrote:
Just a vote for still allowing for multiple genomes in a Seqinfo object (in a
GRanges object). My use case is in bisulfite-sequencing experiments where there
is often a spike-in of a lambda phage genome along with the genome of interest
(human or
? Otherwise this information might be hidden
in the …
Cheers,
Pete
On 09/09/2014, at 9:44 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 09/08/2014 02:28 PM, Peter Hickey wrote:
Just a vote for still allowing for multiple genomes in a Seqinfo
] IRanges_1.99.25 S4Vectors_0.1.5 BiocGenerics_0.11.4
loaded via a namespace (and not attached):
[1] stats4_3.1.0
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] ggplot2_1.0.0 RSQLite_0.11.4
DBI_0.2-7 BiocGenerics_0.11.4
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On 07/28/2014 07:52 PM, Michael Lawrence wrote:
Thanks, should be fixed in devel S4Vectors.
Indeed. Thanks!
H.
On Mon, Jul 28, 2014 at 6:46 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
Works if the DataFrame has columns:
library(IRanges
Hi Henrik,
On 07/24/2014 06:03 AM, Henrik Bengtsson wrote:
On Thu, Jul 24, 2014 at 3:16 AM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Andrzej,
On 07/22/2014 02:28 PM, Andrzej Oleś wrote:
Hi Hervé,
thank you for the demo! Yes, this is definitely much more clear than
just a different color
on this aspect of it.
Please feel free to try switchr out, any feedback is appreciated.
~G
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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
after BioC2014.
Dan
- Original Message -
From: Julian Gehring julian.gehr...@embl.de
To: Hervé Pagès hpa...@fhcrc.org, Michael Lawrence
lawrence.mich...@gene.com, Vincent Carey
st...@channing.harvard.edu
Cc: bioc-devel@r-project.org
Sent: Tuesday, July 22, 2014 8:07:29 AM
Subject: Re
]]
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mailing list
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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
]]
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, Hervé Pagès wrote:
On 05/05/2014 02:12 PM, Cook, Malcolm wrote:
On 05/05/2014 01:00 PM, Cook, Malcolm wrote:
Wondering,
Is it too off the beaten track to expect
`mcols-`(x,NULL)
args(`mcols-`)
function (x, ..., value)
Arguments after the ellipsis must be named
.
science.biology.informatics.conductor
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Fred
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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
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