Let me rephrase this slightly. From one POV the purpose of GenomeInfoDb is
clean up the seqinfo slot. Currently it does most of the cleaning, but it
does not add seqlengths.
It is clear that seqlengths depends on the version of the genome, but I
will argue so does the seqnames. Of course, for
It would be nice (for a number of reasons) to have chromosome lengths
readily available in a foundational package like GenomeInfoDb, so that,
say,
data(seqinfo.hg19)
seqinfo(myResults) - seqinfo.hg19[ seqlevels(myResults) ]
would work without issues. Is there any particular reason this couldn't
That would be perfect actually. And it would radically reduce modularize
maintenance. Maybe that's the best way to go after all. Quite sensible.
--t
On Jun 3, 2015, at 12:46 PM, Vincent Carey st...@channing.harvard.edu wrote:
It really isn't hard to have multiple OrganismDb packages in
Hi all,
Yes, I know 5.3 is old, but it's a system I have to work with at present.
I have the latest supported xlC + friends. gcc building is not an option on
this system for other reasons.
I have read the install instructions and set the env vars according to those
and also am using the
It really isn't hard to have multiple OrganismDb packages in place -- the
process of making new ones is documented and was given as an exercise in
the EdX course. I don't know if we want to institutionalize it and
distribute such -- I think we might, so that there would be Hs19, Hs38,
mm9, etc.
I typically get this info from Homo.sapiens. The result is parasitic on
the TxDb that is in there. I don't know how easy it is to swap alternate
TxDb in to get a different build. I think it would make sense to regard
the OrganismDb instances as foundational for this sort of structural data.
On
Right, I typically do that too, and if you're working on human data it
isn't a big deal. What makes things a lot more of a drag is when you work
on e.g. mouse data (mm9 vs mm10, aka GRCm37 vs GRCm38) where Mus.musculus
is essentially a build ahead of Homo.sapiens.
R seqinfo(Homo.sapiens)
Seqinfo
Dear Bioc annotation team,
Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for
BRCA1; ENSG0012048; entrez:672
via
genes(TxDb.Hsapiens.UCSC.hg38.knownGene, vals=list(gene_id=672))
gives me:
GRanges object with 1 range and 1 metadata column:
seqnames
Duncan Murdoch writes:
On 02/06/2015 11:05 AM, Dirk Eddelbuettel wrote:
Hi Kurt,
On 1 June 2015 at 14:02, Kurt Hornik wrote:
| peter dalgaard writes:
|
| On 30 May 2015, at 01:20 , Imanuel Costigan i.costi...@me.com wrote:
|
| So I assume this commit means NEWS.md is now no longer
This document indicates how to achieve reproducibility independent of the
underlying physical environment.
http://cran.r-project.org/web/packages/doRNG/vignettes/doRNG.pdf
Let me know if that satisfies the question.
On Wed, Jun 3, 2015 at 5:32 AM, Yu, Guangchuang g...@connect.hku.hk wrote:
Hi all,
I have a C function, say Cfun, that calls Lapack's DGEMM routine and I need
to create a shared library to use Cfun inside R. The C file is the following
#includestdio.h
#includeR.h
#includeR_ext/Lapack.h
void Cfun(double *res, double *X, int *n, int *q)
{
char *ptr_TRANSA,
Dear all,
I have an issue of setting seed value when using parallel package.
library(parallel)
library(digest)
set.seed(0)
m - mclapply(1:10, function(x) sample(1:10),
+ mc.cores=2)
digest(m, 'crc32')
[1] 4827c80c
set.seed(0)
m - mclapply(1:10, function(x) sample(1:10),
+
I found the actual reason: I was really stupid.
At the time of testing, I had killed the internet acces.
Sorry for bothering you all ...
Berry
PS: If you want to know why on earth I did that:
Yesterday, I got the error: unable to connect to CRAN.R-project.org on port 80.
I couldn't find an
Hi, this question belongs on R-help, but perhaps
https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/RngStream.html
will be useful.
Best regards
On Wed, Jun 3, 2015 at 3:11 AM, Yu, Guangchuang g...@connect.hku.hk wrote:
Dear all,
I have an issue of setting seed value when using
Der Vincent,
RNGkind(L'Ecuyer-CMRG) works as using mc.set.seed=FALSE.
When mc.cores changes, the output is not reproducible.
I think this issue is also of concern within the Bioconductor
community as parallel version of permutation test is commonly used
now.
Best Regards,
Guangchuang
On
On 03-06-2015, at 09:48, bstr nicola.lunar...@hotmail.it wrote:
Hi all,
I have a C function, say Cfun, that calls Lapack's DGEMM routine and I need
to create a shared library to use Cfun inside R. The C file is the following
#includestdio.h
#includeR.h
#includeR_ext/Lapack.h
On 03.06.2015 09:48, Berry Boessenkool wrote:
Hi,
after submitting my package update, CRAN (Brian Ripley) found a couple of
warnings / messages.
URLs that are not longer existent, a non-ASCII character from copypasting,
incorrect title case.
Stuff that I should and could definitely solve
Ludwig,
If you do this search on the UCSC genome browser (which this annotation
package is built from), you will see that the longest variant is what is
shown
For this situation, generate the permutation indexes outside of the
mclapply, and the do mclapply over a list with the indices.
And btw., please don't use set.seed inside a package; that control should
completely be left to the user.
Best,
Kasper
On Wed, Jun 3, 2015 at 7:08 AM, Vincent Carey
On Wed, 2015-06-03 at 09:51 +0200, Uwe Ligges wrote:
On 03.06.2015 09:48, Berry Boessenkool wrote:
Hi,
after submitting my package update, CRAN (Brian Ripley) found a couple of
warnings / messages.
URLs that are not longer existent, a non-ASCII character from copypasting,
Dear all,
I am writing a package that contains some binaries that should be
linked in /usr/bin after the package
has been installed (I placed them in Rpackage/inst/bin)
I know I can use a script configure or configure.win to be run
before the package has been installed, is there a way I can write
Hi all,
I am developing a package for the interpretation of mass spectrometry data,
which can be found here: https://github.com/goat-anti-rabbit/labelpepmatch.R
I wrote a vignette that compiles fine into a .html using knitr in Rstudio.
The output line in the vignette.rmd file looks like :
There is one possible solution posted in
http://stackoverflow.com/questions/30610375/how-to-run-permutations-using-mclapply-in-a-reproducible-way-regardless-of-numbe/30627984#30627984
.
As Kasper suggested, it's not a proper way to use set.seed inside a package.
I suggest using a parameter for
There are different ways set.seed can be used. The way it is suggested on
the aforementioned stackoverflow post is basically a two stage process.
First seed is provided by a user (set.seed(1)). That is user can change
the outcome from run to run. Based on that seed, a vector of randomized
seeds
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