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_1.13.2' and pushed it to
> bioc-devel,
On Tue, Mar 25, 2014 at 9:31 AM, Peter Haverty wrote:
> One benefit of having dimnames on assays would be that one could use
> DataFrames as assays, like in eSet. My genoset class is becoming more and
> more like SummarizedExperiment. The dimname issues prevent me from
> switching entirely from e
Hi,
This discussion went off-line and I wanted to give a summary of what we
decided to go with.
We'll create a new package, BiocFile, that has a minimal API.
API:
- 'File' class (virtual, reference class) and constructor
- close / open / isOpen
- import / export
- file registry
We won't requ
Hi Ilari,
org.Hs.eg.db is one of the packages included in Homo.sapiens and it's
the origin of 'MAP'. This variable maps between entrez gene ids and
cytoband names, not genomic coordinates (as you've discovered). It
includes bands and sub-bands provided by Entrez Gene downloaded from here:
Also, keeping just the colnames would be sufficient to put a DataFrame in
SE's assays. DataFrames need to have colnames, but can have NULL rownames
(right?).
BTW, BigMatrix also has the argument "withDimnames" for subsetting. Adding
dimnames to ( and copying ) a huge vector takes as much time as p
If it makes genosets coercible into SEs then I'm all for the change and its
permanence
--t
> On Mar 25, 2014, at 9:31 AM, Peter Haverty wrote:
>
> One benefit of having dimnames on assays would be that one could use
> DataFrames as assays, like in eSet. My genoset class is becoming more and
>
One benefit of having dimnames on assays would be that one could use
DataFrames as assays, like in eSet. My genoset class is becoming more and
more like SummarizedExperiment. The dimname issues prevent me from
switching entirely from eSet to SummarizedExperiment.
I think that keeping only one cop
Hi Ryan,
Thank you for the detailed bug report and already providing a fix for
this. I have added your patch to 'les_1.13.2' and pushed it to
bioc-devel, the updated build should become available soon.
I'll do some more tests within the next days, and then also update
bioc-release. If you need
