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On 10/29/2014 01:07 PM, Vincent Carey wrote:
On Wed, Oct 29, 2014 at 2:15 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi,
On 10/28/2014 08:51 PM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès
mailto:hpa...@fredhut
Hi,
On 10/28/2014 08:51 PM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
On 10/28/2014 12:42 PM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès
mailto:hpa...@fredhut
On 10/28/2014 12:42 PM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès 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 <
kasperdanielhan...@
ilman/listinfo/bioc-devel
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[15] fail_1.2 foreach_1.4.2
[17] GenomicAlignments_1.2.0 GenomicFeatures_1.18.0
[19] iterators_1.0.7 RCurl_1.95-4.3
[21] RSQLite_0.11.4 rtracklayer_1.26.0
[23] sendmailR_1.2-1 stringr_0.6.2
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[27] zlibbioc_1.12.0
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suggestion?
Mike
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quot;, "X", "I", "D")
}
cigarRangesAlongReferenceSpace(cigar, flag = NULL, pos = pos,
f = f, ops = ops, drop.empty.ranges = FALSE, reduce.ranges = TRUE)
}
What is the rationale for setting `drop.D.ranges` by default to FALSE?
Because last time I
g the man pages for these internal helpers.
Co-developers of your 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
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;s important?
What has changed is that now 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 mailto:hpa...@fhcrc.org>> wrote:
new warning more to the point.
H.
Michael
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cn or jiaoyinm...@picb.ac.cn
Mob: +86 1852139 6188
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me reference*
* genome (use suppressWarnings() to suppress this warning).*
*It seems to me that if we can check equality of the assigned genomes, we
should*
*not issue this warning.*
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Bioc-de
th x
being a GRanges object, an entire package loading sequence starts:
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
[... etc ...]
which may look a bit odd to the user. for every other
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le to deal with gzipped fasta files these days.
Thanks,
Florian
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R.methodsS3_1.6.1
[61] R.oo_1.18.0 Rsamtools_1.16.1
rtracklayer_1.24.2
[64] R.utils_1.33.0 scales_0.2.4 sendmailR_1.1-2
[67] splines_3.1.0stats4_3.1.0 stringr_0.6.2
[70] survival_2.37-7 tools_3.1.0
VariantAnno
was
breaking the attract package in some obscure way.
The warnings you get when you load ReportingTools 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.
__
f(), not the IRanges/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
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wrote:
On Tue, Sep 9, 2014 at 12:30 AM, Hervé Pagès 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
ise this information might be hidden
in the "…"
Cheers,
Pete
On 09/09/2014, at 9:44 AM, Hervé Pagès 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 Seqin
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 mou
nal function singleGenome() to take care of this.
On Mon, Sep 8, 2014 at 10:50 AM, Hervé Pagès 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
ot;"dm3""dm3""dm3"
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:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] 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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5.13
GenomicRanges_1.17.28 GenomeInfoDb_1.1.18
[17] IRanges_1.99.24S4Vectors_0.1.2
fastcluster_1.1.13 reshape2_1.4
[21] ggplot2_1.0.0 RSQLite_0.11.4
DBI_0.2-7 BiocGeneric
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 mailto:hpa...@fhcrc.org>> wrote:
Hi Michael,
Works if the DataFrame has columns:
library(IRanges)
vector with out-of-bounds TRUE values
This currently causes subset() to fail on a GRanges object with no
metadata cols.
Thanks,
H.
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which are just TranscriptDb objects wrapped
into packages. So I guess it's time to rename the TranscriptDb
class -> TxDb.
Cheers,
H.
Michael
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publicly soon, but since it is so on-topic I figured I'd give this list a
heads-up on this aspect of it.
Please feel free to try switchr out, any feedback is appreciated.
~G
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Hi Henrik,
On 07/24/2014 06:03 AM, Henrik Bengtsson wrote:
On Thu, Jul 24, 2014 at 3:16 AM, Hervé Pagès 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. Maybe we could
.
Cheers,
Andrzej
On Tue, Jul 22, 2014 at 10:04 PM, Hervé Pagès wrote:
Hi Andrzej,
On 07/22/2014 10:14 AM, Andrzej Oleś wrote:
Hi all,
I think having links is useful, e.g. for someone who uses BioC release
but wants to install by hand a particular package from the devel
branch.
Distinct
do probably won't happen until after BioC2014.
Dan
- Original Message -
From: "Julian Gehring"
To: "Hervé Pagès" , "Michael Lawrence"
, "Vincent Carey"
Cc: bioc-devel@r-project.org
Sent: Tuesday, July 22, 2014 8:07:29 AM
Subject: Re: [Bioc-deve
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NA NA ... NA
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just the function for using a Snow-based BiocParallel::blapply(). The
original package would take too long to load (around 40 secs, it used
to import a total of 18 packages) and this has a very large impact
compared to used a multicore-based blapply(). However, the Snow-based
version uses signi
g/gmane.
science.biology.informatics.conductor
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ng a patch for this, please let me know.
Best wishes
Julian
On 05.05.2014 23:29, 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
>>
>>
.
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from scratch anyway then it would make sense to use
SEXP-based memory, or even better, to put a thin abstract layer between
the algo itself and memory management so they are decoupled.
Cheers,
H.
On Tue, Jul 1, 2014 at 9:05 AM, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote:
Hi Hector,
istinfo/bioc-devel
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ioMart.plantsmart21 package in devel will also
get the sequence lengths when we re-generate it but this will only
happen a few weeks before the BioC 3.0 release (and at that time it
might become TxDb.Athaliana.BioMart.plantsmart22).
Cheers,
H.
Vince
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ake the seqlevelsStyle() setter work directly on the
SNPlocs.Hsapiens.dbSNP.20120608 object itself will take more time
though. It'll actually be part of some more important SNPlocs
refactoring plans I've had on my list for a while now. Won't happen
before a couple of months.
Cheers,
H.
he bioconductor list
about 1 year ago:
https://stat.ethz.ch/pipermail/bioconductor/2013-July/054056.html
Cheers,
H.
Michael
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1
, what about adding support for atomic vectors, in
addition to Rles? Also, what about functions that are optimized for
partitionings? Those would be easy to write and would let us greatly
accelerate e.g. sum,CompressedIntegerList. Right now we rely on rowsum()
which is fast but could be much faster.
Micha
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aring than what we have right now. Will have to dig
into this a little bit more. Won't happen before a couple of weeks
though.
H.
Thanks,
Michael
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Hi Peter,
On 05/26/2014 04:37 PM, Peter Hickey wrote:
Thanks for the suggested work-around, Martin. In order to define the method on the group
generic 'Ops' rather than '==' I will need to generalise .MTuples.compare to the 'Arith',
'Compare' and 'Logic' sub-groups listed in ?Ops, won't I? I'l
query.
Good. nearest() between a GRanges and a GRangesList is the easy one:
togroup(subject, nearest(query, unlist(subject, use.names=FALSE)))
Is this doing what you need?
Cheers,
H.
-Ryan
On Fri 23 May 2014 11:13:24 AM PDT, Hervé Pagès wrote:
Hi Ryan,
On 05/22/2014 03:38 PM, Ryan C. Tho
? Can't
think of a use case for that one. Finding the nearest gene or transcript
for junction reads?
Thanks,
H.
-Ryan
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On 05/20/2014 12:49 PM, Hervé Pagès wrote:
Hi Julian,
At the root of the problem is what rbind() does on DataFrames containing
matrices:
m <- matrix(1:4, nrow=2)
df <- DataFrame(m=I(m))
df2 <- rbind(df, df)
Then:
> df2
DataFrame with 8 rows and 1 column
## matrix first, vector second fails
mcols(gr1) = mcols(gr2) = DataFrame(m = I(m), x = 1)
c(gr1, gr2) ## fails
#+END_SRC
Best wishes
Julian
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Please let me know if you have questions or concerns about this.
Thanks,
H.
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Ph
On 05/12/2014 12:23 PM, Michael Lawrence wrote:
On Mon, May 12, 2014 at 11:41 AM, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote:
Hi Michael,
On 05/09/2014 04:39 PM, Michael Lawrence wrote:
What would be the fastest way to do this with a DNAString? J
#x27;t seem that the memory
the returned external pointer is pointing to (a struct twoBit) 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 thousand
lently turning everything
that is not A, C, G, T, or N into a T?
Thanks,
H.
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E-mail: hpa...@fhc
On 05/08/2014 05:00 PM, Dario Strbenac wrote:
We could simply remove the GDL2GRL function once the GenomeData and
GenomeDataList are defunct.
Sounds good.
H.
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On Thu, May 8, 2014 at 3:32 PM, Hervé Pagès 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 w
re are significant benefits in using
GenomeData/GenomeDataList over GRanges/GRangesList.
Thanks,
H.
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E-mail:
mcols(x)
ans
}
)
###
Kind regards,
Sebastian
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Fr
as *the* idiom. Its only advantage
is that it doesn't introduce a new symbol.
H.
>
>Nothing we can do about this.
>
>Cheers,
>H.
>
>>
>> to work?
>>
>> hint: it does not
>>
>> >-Original Message-
>> &
.
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
>Cc: Johnsto
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it goes.
Thanks,
Michael
On Tue, Apr 29, 2014 at 11:24 PM, Hervé Pagès 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
h 5 rows and 1 column
score
1NA
2NA
3 TRUE
4 TRUE
5 FALSE
How hard it would be to bring the rbind,DataFrame method in line with
rbind.data.frame?
Thanks,
H.
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F
ers/how-to/deprecation/
package 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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ndmailR_1.1-2 stats4_3.1.0
#[22] stringr_0.6.2 tools_3.1.0 zlibbioc_1.10.0
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Hi Tengfei,
On 04/23/2014 02:28 PM, Tengfei Yin wrote:
Hi all,
I found IRanges:::safeExplode() removed, is there any recommended
alternative method I should use to replace it?
It's in S4Vectors now.
Cheers,
H.
thanks
Tengfei
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Hi Vince,
On 04/17/2014 04:19 AM, Vincent Carey wrote:
On Thu, Apr 17, 2014 at 2:37 AM, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote:
Hi Vince,
On 04/10/2014 08:16 AM, Vincent Carey wrote:
seems like something we should use more routinely, and it w
el Lawrence
*发送时间：* 2014-04-17 05:15:10
*收件人：* Herv開Pag鑣
*抄送：* liyangbjmu; maintainer; bioc-devel@r-project.org
*主题：* Re: [Bioc-devel] [devteam-bioc] suggestion about
bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38
Another interesting aspect of 2bit is that it supports simple masking.
I'm all f
one: (206) 667-5791
Fax:(206) 667-1319 <%28206%29%20667-1319>
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_
s possible,
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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H.
On Wed, Apr 16, 2014 at 12:59 PM, Hervé Pagès 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
hanks,
H.
Best,
Sean
2014-04-16
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attached packages:
[1] GenomicRanges_1.15.44 GenomeInfoDb_0.99.31 IRanges_1.21.45
[4] BiocGenerics_0.9.3
loaded via a namespace (and not attached):
[1] stats4_3.1.0 XVector_0.3.7
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(617)
depend on a BioC package.)
Even with BiocGenerics around, it's hard to avoid this kind of clash.
H.
Best wishes,
Laurent
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1.23.22 sendmailR_1.1-2
[25] stats4_3.1.0 stringr_0.6.2
[27] tools_3.1.0 zlibbioc_1.9.0
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P.O. Box 19024
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E-mail: hpa...@fhcrc
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 mailto:hpa...@fhcrc.org>> wrote:
On 04/01/2014 02:43 PM, Michael La
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattl
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, I'm not totally
convinced by the names. What about phead() and ptail() ("p" for
"parallel"), or vhead() and vtail() ("v" for "vectorized"), or mhead()
and mtail() (they're just fast equivalent to 'mapply(head, x, n)' and
'mapply(tail,
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