Picking up this thread in lack of other places (= were should
BiocParallel be discussed?)
I saw Martin's updates on the BiocParallel - great. Florian's SGE
scheduler was also mentioned; is that one built on top of BatchJobs?
If so I'd be interested in looking into that/generalizing that to work
w
Hoping to use Sanger's COSMIC database ("Catalogue Of Somatic Mutations In
Cancer") via biomaRt, I ran into some trouble: 'CosmicMart' connections usually
fail. A few lines to replicate the problem are included below. SessionInfo
output follows.
- Paul
library(biomaRt)
tbl <- listMarts
Bioc Developers --
BiocParallel generated quite a bit of discussion, so I'm providing a brief
update. Version 0.0.5 is available to R-devel users via biocLite; it's in svn
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel
and github
https://github.com/Bioconductor/
Parsing a trackHub turns out to be relatively casual, at least if the hub
is well behaved. (If it isn't, must not be worthwhile... ;-))
R> dim(hubTracks)
[1] 11144 2
So that's a hub with 11144 tracks, which takes a while to parse (perhaps
2-3 minutes). There are a bunch of flat tracks right
On Sun, Dec 2, 2012 at 3:43 PM, Tim Triche, Jr. wrote:
> So, a trackHub as spec'd by UCSC ends up being a DAG. It may not be
> strictly directed, even; I'm pondering that. The file under a hub's root
> is title genomesall.txt and tells what trackDb is associated with a genome.
> Loading the cor
If you want to do this, you need to use grid.
The question is whether it is worth your time, if you're not already
experienced with grid. Murrell's book is a good place to start (or
the vignettes in grid).
Kasper
On Mon, Dec 3, 2012 at 4:47 AM, Servant Nicolas
wrote:
> Hi all,
>
> I have 4 mat
Hi all,
I have 4 matrices that I would like to plot together (as heatmaps)
One way to easily do that is to design a layout (or a grid) and to plot them in
each (i,j) cells.
1222
1222
1222
1222
1222
3444
3444
3444
But now, I just want to take the same representati
