On Mon, Jan 7, 2019 at 3:26 PM Henrik Bengtsson
wrote:
>
> 1. To achieve fully numerically reproducible RNGs in way that is
> *invariant to the number of workers* (amount of chunking), I think the
> only solution is to pregenerated RNG seeds (using
> parallel::nextRNGStream()) for each individual
I don't know if this is helpful for BiocParallel, but there's an extension
for the foreach package that ensures reproducible RNG behavior for all
parallel backends: https://cran.r-project.org/web/packages/doRNG/index.html
Perhaps some of the principles from that package can be re-used?
On Mon, Ja
to install it.
For more info, see this old post about the same problem:
https://support.bioconductor.org/p/16932/
Regards,
Ryan
On Thu, May 10, 2018 at 11:58 PM Robert Castelo
wrote:
> hi,
>
> this is a question for limma developers.
>
> at every new fresh installation of BioC
CRAN, the
biocLite.R script will become a thin wrapper around it?
-Ryan
On Wed, May 9, 2018 at 3:29 PM Martin Morgan
wrote:
> Developers --
>
> A preliminary heads-up and request for comments.
>
> Almost since project inception, we've used the commands
>
>source(
ons/BiocFileCache/citation.html>
?
Regards,
Ryan Thompson
On Tue, Apr 17, 2018 at 12:23 PM Ryan Thompson wrote:
> I wasn't specific about what I meant by "structured" because I'm not
> certain what kind of citation data types CiteAs can handle, though I'd
> assume bibt
familiar with the format).
On Tue, Apr 17, 2018 at 11:57 AM Marcel Ramos
wrote:
> Hi Ryan,
>
> Thanks for pointing this out.
>
> I'm not sure what you mean by "structured" or "format". We do have
> public facing citations
> which can be found at:
&g
hich isn't really an option for a web service like
this, which wants to return a result quickly. Does anyone know a good way
to access this info?
Thanks,
Ryan Thompson
[[alternative HTML version deleted]]
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t the need for separate installation of other command-line tools.
Regards,
Ryan Thompson
On Sun, Nov 12, 2017 at 2:12 PM Ioannis Vardaxis
wrote:
> Hi,
> I have developed a package and is current under review from
> Bioconductor. In the future I am considering of making some chang
the function/argument
names I've provided are just example names.
Anyway, I'm not very experienced designing object-oriented interfaces in R,
but that's my 2 cents from a user perspective of how I would expect such an
R package to work. Hopefully others with more class design e
I think the main reason for reusing/subclassing core classes that users can
appreciate is that it makes it much easier for users to integrate multiple
packages into a single workflow. Only the most basic of pipelines uses just
a single Bioconductor package. For instance, an "edgeR" pipeline obvious
rlaps will fail and error, and
occasionally R will segfault. Since the bug is random, I've also included a
transcript of me running the script until it crashes, as well as a text
file with the traceback in it.
Can you help me debug the issue here?
Thanks,
-Ryan
[[alternative
They wouldn't be exactly consistent even if they used the same prior count,
since the calculations are not identical. edgeR normalizes the prior count
by each library's normalization factor so that log fold changes are always
squeezed toward zero, while voom, if I understand correctly, does not
nor
s. But even for that case, fixed-wdith ranges are not
necessarily usable because a position less than 1kb from the end of a
chromosome would require a truncated range. (What behavior would we
expect from a hypothetical FWRanges class in this case?)
-Ryan
On 11/23/16 8:01 PM, Ryan wrote:
Is it po
Is it possible to allow the width slot of IRanges to be either a normal
vector or an Rle?
On 11/23/16 6:18 PM, Peter Hickey wrote:
I've been toying with the idea of a fixed/constant width Ranges
subclass. The motivation comes from storing DNA methylation data at CH
loci (non-CpG methylation):
.
I leave it up to the developers of the SRAdb package to decide whether
or not this is a bug, but I think it should at least be documented that
the sort order of the output of sraConvert is arbitrary and will not
necessarily match the input.
-Ryan
ion" dialog when a user tries to write in the
answer box for their own question.
Thanks,
-Ryan
P.S. I hope bioc-devel is the right place to ask about how to do
moderation on the support site.
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it for anything.
If anyone's interested, you can get it here:
http://mneme.homenet.org/~ryan/SubsettableListOfArrays.R
-Ryan
On 9/18/15 7:41 PM, Michael Lawrence wrote:
> While it's useful (and often necessary) to store the big matrices out
> of core, it would be convenient to s
In the dev version, SummarizedExperiment has been split into
RangedSummarizedExperiment (equivalent to the current
SummarizedExperiement, with rowRanges) and SummarizedExperiment (kind of
like eSet, no rowRanges). Given that eSet objects also support multiple
assayData elements, I believe the n
mma/
Hopefully this can be fixed soon.
-Ryan
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mehow digest must have been installed in /usr/local but not pkgmaker,
so removing it broke the dependency chain. No idea how it got into that
state, but problem solved.
On 8/7/15 5:06 PM, Martin Morgan wrote:
On 08/07/2015 04:31 PM, Dan Tenenbaum wrote:
- Original Message -
From: &q
Konsole output Hello,
I was recently setting up the latest version of R & Bioc on a system,
installing all packages from scratch, and I ran into an error while
installing bumphunter. It failed to install because it couldn't load the
"digest" package. After installing this package manually, bump
From base, according to my R console:
> subset
standardGeneric for "subset" defined from package "base"
function (x, ...)
standardGeneric("subset")
Methods may be defined for arguments: x
Use showMethods("subset") for currently available ones.
On 07/29/2015 10:40 AM, Steve Lianoglou wrote:
Actually, the code looks like it should be adding these names, so I need to
go back through my code and get back to you on that issue.
On Jul 7, 2015 9:58 AM, "Ryan C. Thompson" wrote:
> I've also encoundered another problem, this time I believe related to a
> change the t
0.2.5
[25] codetools_0.2-11 oligoClasses_1.30.0 MASS_7.3-41
[28] GenomicRanges_1.20.5 colorspace_1.2-6 stringi_0.5-2
[31] munsell_0.4.2 affyio_1.36.0
On 07/07/2015 06:52 AM, Matthew McCall wrote:
Ryan,
Thanks for pointing these out. I'll look into them soon, but I imagine
your assessment is correc
o ifelse will have length zero and "ifelse" does NOT do lazy
evaluation.
On 07/06/2015 12:21 PM, Ryan C. Thompson wrote:
Hello,
I just encountered a bug in frmaTools that makes it impossible to use
on certain array platforms. The following lines in
makeVectorsAffyBatch fail on an
t; "1e+05" "4e+05"
As you can see, the problem is that as.character will happily use
scientific notation when it feels like it, which then fails a test for
string equality. I believe the solution is to replace that test with:
all(sprintf("%i", pmi) == rownames(pms))
-Ryan
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Oh wow, I didn't know you could put a DataFrame into a single column of
another DataFrame. That actually solves a problem for me too (I don't
intend to expose nested DataFrames to the users though).
On 6/17/15 7:23 PM, Martin Morgan wrote:
On 06/17/2015 11:41 AM, davide risso wrote:
Dear list
Thanks Ivana,
I've forwarded your message to the bioc-devel list so graphite
developers can see it.
-Ryan
On 06/16/2015 12:46 PM, ihnat...@iba.muni.cz wrote:
Hello,
this problem is caused by the presence of interaction type
"control(In(INHIBITION-COMPETITIVE))" which is
This is great to hear. I sometimes want to delve into the source code of
a package's internals, but doing so through the SVN web interface is
clunky. Being able to use Github's repo browsing functionality for Bioc
packages is great.
On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear Bioconduct
iens", "reactome")["Insulin receptor
signalling cascade"],
"test", TRUE)
1: prepareSPIA(pathways("hsapiens", "reactome")["Insulin receptor
signalling cascade"],
"test", TRUE)
I guess for now I will remove
, I'm interested to see what you come up with.
Michael
On Thu, Apr 23, 2015 at 4:06 PM, Ryan C. Thompson
wrote:
> Hi all,
>
> So, dplyr is a pretty cool thing, but it currently works with data.frame
> and data.table, but not S4Vectors::DataFrame. I'd like to change that if
&g
start, and I expect
things might be complicated because dplyr uses S3 and S4Vectors uses S4.
Can anyone offer any pointers?
-Ryan
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tq assuming it can read from connections
> rather than just files, but I have not tested it to be sure.
>
> On Wed, Apr 22, 2015 at 1:16 PM, Ryan C. Thompson
> mailto:r...@thompsonclan.org>> wrote:
>
> That's not ideal because it's duplicating storag
That's not ideal because it's duplicating storage unnecessarily.
On 04/22/2015 04:07 AM, Aedin wrote:
This is one instance were a system or simple unix command is very easy
system('cat *.fastq > all.fastq')
---
On Apr 22, 2015, at 6:00, bioc-devel-requ...@r-project.org wrote:
Re: Append/co
s files one-by-one in a loop with append=FALSE for the first file
and append=TRUE for the rest. (Also appending to a compressed fastq
might not work?)
-Ryan
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Yes, a single-assay SummarizedExperiment would be the most common case
for unnamed assays. But I think at the very least there should be a
warning on unnamed assays.
On 3/12/15 9:24 AM, Martin Morgan wrote:
On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said
This doesn't make any sen
I thought CRAN packages weren't allowed to depend on Bioconductor
packages for exactly this reason.
On 03/02/2015 03:18 PM, Laurent Gatto wrote:
Dear all,
I had never realised that CRAN packages that depended on Bioc packages
could actually not be installed with install.packages without setti
g package
building, if that's possible.
Thanks,
-Ryan Thompson
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o people implementing plots to also
implement a way to get the plot data.
-Ryan
On Fri 31 Oct 2014 03:43:04 PM PDT, Steve Lianoglou wrote:
Hi,
On Fri, Oct 31, 2014 at 2:35 PM, Thomas Lin Pedersen
wrote:
With regards to abstraction - I would personally much rather read and write
code that c
e here, and I
would have either reported it with a patch or explained what I tried
and where I got stuck.
-Ryan
On Mon 06 Oct 2014 05:55:02 PM PDT, Michael Lawrence wrote:
Makes sense to me. Just wondering: if S4Vectors were say on github,
would this be something that you would be comfortable res
Hi,
I've just noticed that DataFrame doesn't have a "droplevels" method, but
"data.frame" does. In fact, "droplevels.data.frame" seems to work just
fine on DataFrame objects. Could this be added?
-Ryan
> sessionInfo()
R version 3.1.0 (2014-04-10)
y have any experience with svn or with
git-svn, but this seems like exactly the use case for it.
-Ryan
On Fri 05 Sep 2014 04:50:49 PM PDT, Peter Haverty wrote:
Hi all,
I respectfully disagree. One should certainly check in each discrete unit
of work. These will often not result in something tha
q file was delegated
to a subprocess. So my solution also doesn't generalize to multi-step
parallel pipelines.
Thanks,
Jeff
-Ryan
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up in '...'.
Any function/method called inside summarizeOverlaps() with a '...'
will pass the arguments down; they continue to be passed down until
they are explicitly stated in a function signature (e.g., 'width' and
'fix' in ResizeReads()).
Valerie
On
o reflect this?
On Wed Aug 6 11:21:20 2014, Valerie Obenchain wrote:
Hi Ryan,
On 08/05/2014 05:47 PM, Ryan C. Thompson wrote:
Hi again,
I'm looking at the examples in the summarizeOverlaps help page here:
http://www.bioconductor.org/packages/devel/bioc/manuals/GenomicAlignments
ads function should be required to
only take one argument, or else the method of passing through
additional arguments to it should be documented.
-Ryan
On Tue 05 Aug 2014 05:12:41 PM PDT, Ryan C. Thompson wrote:
Hi Valerie,
I got really busy around May and never got a chance to thank you f
Hi Valerie,
I got really busy around May and never got a chance to thank you for
adding this option to summarizeOverlaps! So thank you!
-Ryan
On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote:
GenomicAlignments 1.1.8 has a 'preprocess.reads' argument. This should
be
I just want to add the perspective that I often browse package
documentation & vignettes from the website rather than accessing it from
the R command line. Sometimes it's just easier or more convenient to
view it in a browser. So, when doing this, I sometimes accidentally get
the wrong document
) %*% prior.count.scaled
I downloaded the current development tarball from the Bioconductor site,
and this also seems to have the same issue.
On a side, note, the edgeR page lists 4 maintainers. Which one is the
best one to email about bug reports, or should I cc all of the
these two arguments expect different things" than "this one
argument expects a different thing depending on the value of another
argument".
-Ryan
On Sun Jun 15 11:17:59 2014, Michael Lawrence wrote:
I just thought there is some benefit for the callback to be the same,
regar
, so I basically want to call nearest with a GRanges
of peaks against a GRangesList of TSS (each TSS is a range with a width
of 1 containing the first base pair of a transcript). I don't personally
need a method that works for a GRangesList query.
-Ryan
On Fri 23 May 2014 11:13:24 A
do this by
unlisting the GRangesList, calling nearest, and then post-processing to
figure out which element of the original GRangesList includes the
nearest range, but it would be nice to have a function that already does
this for me.
-Ryan
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l free to eliminate it.
- Do you want to require strand info for all reads? Is this because of
how resize() anchors "*" to 'start'?
Yes, I require strand info for all reads because the reads must be
directionally extended, which requires strand info. Ditto for counting
the 5-pri
No, I forgot to attach the file. Here is the link:
https://www.dropbox.com/s/7qghtksl3mbvlsl/counting-modes.R
On Wed 30 Apr 2014 02:18:28 PM PDT, Valerie Obenchain wrote:
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
you send one?
Thanks.
Valerie
On
nto another function) are
confusing for people who are not programmers by trade. Maybe
summarizeOverlaps should just gain an argument to pass args to findOverlaps.
-Ryan Thompson
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I agree it could be a bit weird, but the merge method will catch any
inconsistency and throw an error, so I think it's fairly safe. And as you
say, the common case should be that the files all have the same seqinfo
anyway.
On Apr 25, 2014 10:32 PM, "Martin Morgan" wrote:
>
s the generic for "List" which gives a useless
result.
seqinfo(fll)
## Now add a method
setMethod("seqinfo", signature=list(x="BamFileList"), function (x)
{
Reduce(merge, lapply(x, seqinfo))
}
)
## Now this returns
That won't work if any vector has fewer than 5 elements. Maybe
lapply(x, head, n=5)
would work?
On Tue Apr 1 09:24:51 2014, Cook, Malcolm wrote:
in the mean time,
lapply(`[`,x,IntegerList(1:5))
??
>-Original Message-
>From: bioc-devel-boun...@r-project.org
[mailto:bioc-devel-b
Thanks! I patched my local copy on my own, so I'll be fine until the next
release.
On Mar 25, 2014 3:04 AM, "Julian Gehring" wrote:
> Hi Ryan,
>
> Thank you for the detailed bug report and already providing a fix for
> this. I have added your patch to 'les_1.13.
ene set is MSigDB ID
"AAAYRNCTG_UNKNOWN", with the gene IDs converted to my organism
(cynomolgus monkey, whose genes are annotated with orthologous Ensembl
Peptide IDs from human & rhesus).
-Ryan
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I would prefer the droplevels method for SummarizedExperiment, since
this is consistent with the use of droplevels on data.frame objects.
On Wed 12 Mar 2014 03:02:37 PM PDT, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’
ob
, 2013, at 5:20 PM, Ryan wrote:
On Mon Dec 16 14:18:41 2013, Steve Lianoglou wrote:
On Mon, Dec 16, 2013 at 2:03 PM, Ryan wrote:
I'm quite sure that it is an interaction between something that xlsxjars
does and edgeR's C code. The example I gave is a reduction from my actual
scr
16 Dec 2013 02:30:34 PM PST, Simon Urbanek wrote:
On Dec 16, 2013, at 5:20 PM, Ryan wrote:
On Mon Dec 16 14:18:41 2013, Steve Lianoglou wrote:
On Mon, Dec 16, 2013 at 2:03 PM, Ryan wrote:
I'm quite sure that it is an interaction between something that xlsxjars
does and edgeR's C
On Mon Dec 16 14:18:41 2013, Steve Lianoglou wrote:
On Mon, Dec 16, 2013 at 2:03 PM, Ryan wrote:
I'm quite sure that it is an interaction between something that xlsxjars
does and edgeR's C code. The example I gave is a reduction from my actual
script, and I finally figured out th
jars, then everything runs just fine for me.
My current solution is to use the parallel package to load and use the
xlsx package only in subprocesses, so the main R process never uses
java.
-Ryan
On Mon Dec 16 13:19:53 2013, Martin Morgan wrote:
Crashes for me in locfit's C code but in
8txll5vysj/NE8xsa6bxo
Thanks,
-Ryan
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Ok, sorry to bother you. I'll ask my cluster admin for an update.
On Tue Nov 26 17:24:34 2013, Wei Shi wrote:
Hi Ryan,
It seems you are using a quite old version of Subread. The latest version of
SourceForge Subread is 1.4.2 and the latest version of bioc Rsubread is 1.12.3.
These ind
Actually, scratch that. I just tried running subread-buildindex on a
file with only the 20-ish chromosome sequences, and it didn't give the
message about 5 sections, but it still crashed with "Killed" and
exit code 137.
On Tue 26 Nov 2013 05:01:48 PM PST, Ryan C. Thompso
after "Building the index...", it says "Killed", and exits with
code 137.
The genome is unfinished and contains over 90,000 small
scaffolds/contigs. My Subread version is 1.3.3. Is it planned to remove
this limitation in future versions?
-Ryan Thompson
_
Just a note: the foreach package has solved this by providing a
"nesting" operator, which effectively converts multiple nested foreach
loops into one big one:
http://cran.r-project.org/web/packages/foreach/vignettes/nested.pdf
On Thu 14 Nov 2013 09:24:29 AM PST, Michael Lawrence wrote:
I like
The minimize the additional memory used by mclapply, remember that
mclapply works by forking processes, and the advantage of this is that
as long as an object is not modified in either the parent or child,
they will share the memory for that object, which effectively means
that a child process
by using the "Recall" function.
-Ryan
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lelism.
Side note 2: Your original link gave a 404 error because it had the word
"Note" appended to it. Removing this gave a valid link:
https://github.com/duncantl/CodeDepends/blob/forCRAN_0.3.5/R/librarySymbols.R
-Ryan
On 11/4/13, 12:13 PM, Gabriel Becker wrote:
> Ryan,
>
>
easily adapt the same code to return a list of all
packages that a function depends on.
-Ryan
On Nov 4, 2013 11:35 AM, "Michael Lawrence"
wrote:
> The dynamic nature of R limits the extent of these checks. But as Ryan has
> noted, a simple sanity check goes a long way. If what h
ation, so I never have to worry about things being undefined
in the forked subprocess. Therefore I cant really dogfood any of the
stuff that might be implemented as a result of this thread.
-Ryan
On Mon Nov 4 03:48:23 2013, Michael Lawrence wrote:
So what is the best practice for ensuring
function refers
to something in the global env.
On Sun Nov 3 21:14:29 2013, Gabriel Becker wrote:
Ryan (et al),
FYI:
> f
function() {
x = rnorm(x)
x
}
> findGlobals(f)
[1] "=" "{" "rnorm"
"x" should be in the list of globals but it isn'
;ll try to code something up soon.
-Ryan
On 11/3/13, 5:10 PM, Gabriel Becker wrote:
> Henrik,
>
> See https://github.com/duncantl/CodeDepends (as used by used by
> https://github.com/gmbecker/RCacheSuite). It will identify necessarily
> defined symbols (input variables) for code that
13 at 3:04 PM, Ryan mailto:r...@thompsonclan.org>> wrote:
Another potential easy step we can do is that if FUN function in
the user's workspace, we automatically export that function under
the same name in the children. This would make recursive functions
just work, but
Another potential easy step we can do is that if FUN function in the
user's workspace, we automatically export that function under the same
name in the children. This would make recursive functions just work, but
it might be a bit too magical.
On 11/3/13, 2:38 PM, Ryan wrote:
Here'
n in
a similar tryCatch to at least provide a more informative error message
when a subprocess has a missing variable.
-Ryan
withBPExtraErrorText <- function(expr) {
tryCatch({
expr
}, simpleError = function(err) {
if (grepl("^object '(.*)' no
mentation is
a good deal more straightforward than before. To support the
multi-argument bpvectorize, I also added a function "bpmvec", which is
to bpvec as bpmapply is to bplapply.
-Ryan
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As you can see, the
child is always a step or two ahead of the main script, so that whenever
the main script asks for the next yield, it gets it immediately instead
of waiting for the child to read from the disk.
So, is this kind of feature appropriate for inclusion into BioConductor?
Hi Gordon,
Thank you so much! That's exactly what I was looking for.
-Ryan
On Sun 01 Sep 2013 03:15:06 PM PDT, Gordon K Smyth wrote:
Dear Ryan,
See contrastAsCoef() in limma 3.17.23.
Best wishes
Gordon
-
Professor Gordon K Smyth,
Bioinform
matrix (i.e. the part of glmLRT that does all the QR decomposition
stuff). Would you consider splitting this logic into a separate function
that takes a design matrix and contrast matrix and returns the
equivalent reparametrized design matrix and vector of coefficients?
Thanks,
-Ryan
you want to fix them.
-Ryan
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Couldn't one test for existence by trying to open the BamFile object, and
possibly read one sequence (or maybe just read the header since I guess a
valid bam file can contain zero sequences)?
On Jan 7, 2013 1:32 PM, "Henrik Bengtsson" wrote:
> On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme
>
With such a huge difference, I would wonder if the "c" method for
GRanges objects is doing N-1 pairwise merges instead of a single N-way
merge.
On Mon 07 Jan 2013 09:08:28 AM PST, Michael Lawrence wrote:
Would be interesting to do some profiling. Could be the merging of the
sequence info, or t
me code to generate a list of GRanges similar
in size to your blockRanges object, and I'll test them myself.
-Ryan Thompson
On 01/06/2013 06:00 PM, Dario Strbenac wrote:
Hello,
For a not so large list of GRanges:
length(blockRanges)
[1] 4029
class(blockRanges)
[1] "list&q
prove my understanding.
Sincerely,
-Ryan
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vels of "condition" would then be usable
as estimates of the average logCPM for each condition? If so, would
these estimates be any better than simply computing logCPM individually
for each sample and taking the mean of all the samples in each group?
Sincerely,
-Ryan
On Mon 10 Dec
dition to the coefficients in the design matrix, "here are the
available factor levels that you can perform comparisons on", and the
user could pick the ones they are interested in and and add/subtract
them to get the test they want.
What do you think of this idea? Could it work
give different results
depending on whether or not I pool?
-Ryan Thompson
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Perfect, that's just what I wanted for Fastq files. Is there no R
facility for reading unindexed bam?
On Tue 04 Dec 2012 02:47:56 PM PST, Martin Morgan wrote:
On 12/04/2012 01:27 PM, Ryan C. Thompson wrote:
Hi all,
I'm currently experimenting with using quip
(https://github.com/dc
ction that is to mapply as mclapply is to
lapply. I plan to implement a param-generic version called bpmapply,
which may become the backend for bpvectorize.
On Tue 04 Dec 2012 01:15:24 PM PST, Michael Lawrence wrote:
On Tue, Dec 4, 2012 at 12:47 PM, Ryan C. Thompson
mailto:r...@thompsonclan.o
ssion would be ideal, but in the short
term, quip supports decompression to standard output, so if I could have
R read FASTQ or BAM data from an open file handle, I could pipe the
decompressed output to R's FASTQ or BAM reader functions. Does anyone
know if this is possible?
-Rya
One issue that I see is that for some kinds of parallel backends, there
may not be any way for "bpworkers" to return something meaningful. For
example, a backend that submits jobs to a large cluster may not know
exactly how many nodes are in the cluster, and in any case returning the
total numb
On Tue 04 Dec 2012 11:31:59 AM PST, Michael Lawrence wrote:
The name "pvec" is not very intuitive. What about "bpchunk"? And since the
function passed to bpvectorize is already vectorized, maybe bpvectorize
should be bparallelize? I know everyone has different
intuitions/preferences when it comes
ames(fData(y)), c("disp_blind",
"disp_pooled"))]
new("DGEGLM", fit)
}
Note that while I have named the functions like S3 method, I haven't
actually tested whether method dispatch works properly with them or not,
since DESeq uses S4 classes. In my code, I c
On 11/17/2012 08:38 PM, Michael Lawrence wrote:
You can use mclapply via parLapply using the fork backend.
Oh, well, that's new to me. I guess that was added when multicore and
snow were merged into the parallel package? If that's so, then parLapply
is perfectly fine to use. However, I will not
Actually, my previous post had a small bug in it: it would throw an
error when printing a zero-column data frame. The following code fixes this:
print.data.frame <- function(df) {
if (ncol(df) > 0 && require("IRanges")) {
prev.max.print <- getOption("max.print")
on.exit(options(max.pri
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