Good news, the file is in AnnotationHub and can be used from there.
There is a download cost the first time but not subsequently.
library(AnnotationHub)
hub = AnnotationHub()
query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
## note 'AH' number, then...
gtf = hub[["AH63797"]]
Need the path rather than the imported path? use cache(hub["AH63797"])
instead.
Martin
On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
To generate mouse.rda, I used:
library(rtracklayer)
mouse <- readGFF("
ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
")
And then I saved the object as mouse.rda
On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk <khomtchouk...@gmail.com>
wrote:
Here it is:
https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey <st...@channing.harvard.edu>
wrote:
(resending with reply all -- please reply to this one)
Can you say some more about the content of the file? Perhaps it can be
placed in ExperimentHub. "mouse.rda" is not very descriptive. is it
in your github repo?
On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
khomtchouk...@gmail.com> wrote:
I need to include an important .rda file in the /data folder of my
Bioconductor package. However, this .rda file exceeds 5 Mb in size. Do
I
have any other options besides for deleting it?
bohdankhomtchouk$ git push origin master
Counting objects: 65, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (65/65), done.
Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
Total 65 (delta 30), reused 0 (delta 0)
remote: Error: file larger than 5 Mb.
remote:
remote: File name: 'data/mouse.rda'
remote: File size: 12.9 Mb
remote:
remote: Please see Biocondcutor guidelines
remote: https://bioconductor.org/developers/package-guidelines/
remote:
To git.bioconductor.org:packages/geneXtendeR
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:
packages/geneXtendeR'
--
Bohdan Khomtchouk, Ph.D.
AHA Postdoctoral Fellow, Gozani & Assimes Labs
Department of Biology & Department of Medicine
Division of Cardiovascular Medicine
Stanford University
Stanford, CA 94305
https://profiles.stanford.edu/bohdan-khomtchouk
CONFIDENTIALITY NOTICE: Information contained in this me...{{dropped:9}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
The information in this e-mail is intended only for t...{{dropped:17}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
