Sorry, forgot to attach the session info:
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8
Hi all,
I recently upgraded R to 3.5 and use the new release of Bioconductor.
The new version of S4Vectors seems to have problem showing a GRanges
with a meta-data column of a data frame. One simplified example is:
gr <- GRanges('chr2', IRanges(1, 11))
gr$df <- data.frame(a = 32)
rep(gr, 11) ##
One of your cell files is funky
> colSums(exprs(alldata) == 0)
GSM907854.CEL.gz GSM907866.CEL.gz GSM907857.CEL.gz GSM907863.CEL.gz
000 686388
GSM907856.CEL.gz GSM907862.CEL.gz GSM907855.CEL.gz GSM907861.CEL.gz
0
Thanks all -> I definitely see the appeal of vectorization.
I'm going to take a few pokes to do just that.
Best,
Jack
Hervé Pagès wrote:
Hi Jack,
You can use
sapply(seq_along(gr), function(i) print(gr[i]))
instead of
sapply(gr, print)
But yes, as Michael noted, looping on a GRanges or
Hi Christian,
It looks like you have to do
*git pull upstream master *
according to your `git remote -v`.
Regards,
Marcel
On 05/14/2018 04:21 PM, cstrato wrote:
> Dear Nitesh,
>
> Thank you for your fast reply. Here is what I tried now,
> including using 'git pull':
>
> $ cd /Volumes/T3Data
Dear Nitesh,
Thank you for your fast reply. Here is what I tried now,
including using 'git pull':
$ cd /Volumes/T3Data/CRAN/GIT/xps
$ git checkout master
Already on 'master'
Your branch is up-to-date with 'origin/master'.
$ git pull
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Alrea
Yes the .tar.gz file. Thanks! H.
On 05/14/2018 11:37 AM, Jose Die wrote:
Hi Hervé,
You mean the .tar.gz file?
Sorry, first time I’m doing this.
Jose
El 14/5/2018, a las 1:33, Hervé Pagès escribió:
Hi Jose,
Contributed BSgenome packages get added to the repository of
annotation packages
Did you try to ‘git pull’ as mentioned in the error message?
Best,
Nitesh
> On May 14, 2018, at 2:48 PM, cstrato wrote:
>
> Dear GIT experts,
>
> On Saturday I wanted to update my development package to xps_1.41.1, however
> until now it was not updated in the 'Multiple platform build/check
Dear GIT experts,
On Saturday I wanted to update my development package to xps_1.41.1,
however until now it was not updated in the 'Multiple platform
build/check report' although I could confirm the changes with Firefox:
https://github.com/cstrato/xps
For this reason I tried today to update
Hi Hervé,
You mean the .tar.gz file?
Sorry, first time I’m doing this.
Jose
> El 14/5/2018, a las 1:33, Hervé Pagès escribió:
>
> Hi Jose,
>
> Contributed BSgenome packages get added to the repository of
> annotation packages rather than to AnnotationHub (think of
> AnnotationHub as a repo
Hi Jack,
You can use
sapply(seq_along(gr), function(i) print(gr[i]))
instead of
sapply(gr, print)
But yes, as Michael noted, looping on a GRanges or IRanges object
is generally not efficient and should be avoided. There is almost
always a "vectorized" solution and it's generally much fast
Thanks for the feedback so far. If you're interested in trying out the
new package, please
remotes::install_github("Bioconductor/BiocManager")
and then
BiocManager::install(version = "devel") # or 3.7 or 3.8
The essential functionality is
BiocManager::install()
BiocManager::version()
It's possible that you could vectorize this code. Maybe open an issue
on the support site.
On Mon, May 14, 2018 at 7:56 AM, Jack Fu wrote:
> Hi Michael,
>
> Mostly for sending each element of the GRanges object to a custom function
> that runs an identical analysis on each element.
> I have some
Hi Michael,
Mostly for sending each element of the GRanges object to a custom
function that runs an identical analysis on each element.
I have some functions that take as input a single range -> calculate
number of reads that overlap the range -> subset the range into K number
of segments based
Just out of curiosity, why are you looping over a GRanges in the first place?
On Mon, May 14, 2018 at 7:28 AM, Jack Fu wrote:
> Hey all,
>
> I think some of the recent changes to GRanges has affected using the
> apply class functions with GRanges objects:
>
> o GenomicRanges now is a List subcl
Hey all,
I think some of the recent changes to GRanges has affected using the
apply class functions with GRanges objects:
o GenomicRanges now is a List subclass. This means that GRanges objects
and their derivatives are now considered list-like objects (even though
[[ don't work
Dear all,
sorry for the delayed response, due to some unfortunate events I had to
prioritize my family the past week.
You find an RStudio project in a zipped folder on this link :
https://jorismeys.stackstorage.com/s/3ik0vMwsvueuT5a
It contains a script called testOligo.R that can be sourced and
Valerie,
��� Sorry, I think my memory of what the actual problem was was wrong.
I have spoken to the rsvg author and he has now fixed the build of rsvg
in CRAN for OS X. So will that then just get automatically put on your
machines, or else, would it now be possible to manually put it on? Sorr
Please review the package guidelines -
http://bioconductor.org/developers/package-guidelines/
Generally, Bioconductor will insist that the R CMD built package tar.gz be less
than 4MB for software packages (There are some exceptions for data experiment
or annotation packages).
If this is a
Hej!
I get this error on the build page for easyRNASeq on malbec1:
Error: processing vignette 'simpleRNASeq.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 0 milliseconds with 0 out of 0
bytes received
Any idea what is causing this?
Thanks,
Nico
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