On 11/26/2014 07:36 PM, Dan Tenenbaum wrote:
- Original Message -
From: "Martin Morgan"
To: "Dan Tenenbaum"
Cc: "Joachim Schumann" , bioc-devel@r-project.org
Sent: Wednesday, November 26, 2014 5:33:22 PM
Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
On 11/26/2014 10:03 AM, Dan Tene
- Original Message -
> From: "Martin Morgan"
> To: "Dan Tenenbaum"
> Cc: "Joachim Schumann" , bioc-devel@r-project.org
> Sent: Wednesday, November 26, 2014 5:33:22 PM
> Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
>
> On 11/26/2014 10:03 AM, Dan Tenenbaum wrote:
> >
> >
> > - Ori
On 11/26/2014 10:03 AM, Dan Tenenbaum wrote:
- Original Message -
From: "Martin Morgan"
To: "Joachim Schumann" , bioc-devel@r-project.org
Sent: Wednesday, November 26, 2014 9:00:07 AM
Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
On 11/26/2014 01:39 AM, Joachim Schumann wrote:
Hi e
The two objects have conflicting APIs. For example, 1D extraction indexes
into the ranges for a GRanges, but into the columns for a table. So I would
not recommend multiple inheritance. Instead, define something new with the
semantics you want and use composition. Maybe just a subclass of DataFrame
OK, GRanges as vector that does overlap stuff makes sense, but I think
putting a DataFrame of metadata on that confuses the purpose of the
object. How about a "GRangesTable" that inherits from both GenomicRanges
and DataTable? It would be a DataFrame with a fancy index. The DataFrame
API would m
Hi guys,
I like the idea of separating the row data from the row ranges.
This could be formalized with 2 distinct accessors: rowData() and
rowRanges(). The former would return a DataFrame, and the latter
NULL or a range-based object (GRanges or GRangesList).
I don't think there is the need for an
One thing that’s become apparent working on epivizr is that it may be useful to
think about ‘rowData’ in a SummarizedExperiment as having two distinct
components: row coordinates and row metadata. In the current class rowData is a
‘GenomicRanges’ which contains both coordinates (the ranges) and
- Original Message -
> From: "Martin Morgan"
> To: "Joachim Schumann" , bioc-devel@r-project.org
> Sent: Wednesday, November 26, 2014 9:00:07 AM
> Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
>
> On 11/26/2014 01:39 AM, Joachim Schumann wrote:
> > Hi everyone,
> > this morning I got a
GRangesList is very compact, so this would definitely get the job done. But
having an empty range is not the same as a NA, nor does it mean that ranges
are "irrelevant". There are definitely times, especially as we extend
beyond genomics, when we need something more general, as Pete suggests.
As a
so as a simple experiment, I did the following:
library(GenomicRanges)
bar <- matrix(rnorm(100), ncol=10)
colnames(bar) <- as.character(1:10)
rownames(bar) <- letters[1:10]
foo <- SummarizedExperiment(assays=list(bar=bar))
rowData(foo)
## GRangesList object of length 10:
## $a
## GRanges object w
On Wed, Nov 26, 2014 at 9:07 AM, Peter Haverty
wrote:
> Hi all,
>
> I believe there is a strong need for an object that organizes a collection
> of rectangular data (matrices, etc.) with metadata on the rows and
> columns. Can SummarizedExperiment inherit from something simpler that has
> a Data
Hi all,
I believe there is a strong need for an object that organizes a collection
of rectangular data (matrices, etc.) with metadata on the rows and
columns. Can SummarizedExperiment inherit from something simpler that has
a DataFrame as rowData? (I believe GenomicRanges should inherit from
Dat
On 11/26/2014 01:39 AM, Joachim Schumann wrote:
Hi everyone,
this morning I got an email from bioconductor.
The message:
According to the "Build/check report" for BioC 3.0,
the flowCHIC package has the following problem(s):
ERROR for 'R CMD check' on zin1.
The error I get is the following:
Err
On 26 November 2014 14:59, Wolfgang Huber wrote:
> A colleague and I are designing a package for quantitative proteomics
> data, and we are debating whether to base it on the
> SummarizedExperiment or the ExpressionSet class.
>
> There is no immediate use for the ranges aspect of
> SummarizedExpe
A colleague and I are designing a package for quantitative proteomics data, and
we are debating whether to base it on the SummarizedExperiment or the
ExpressionSet class.
There is no immediate use for the ranges aspect of SummarizedExperiment, so
that would have to be carried around with NAs,
Hi everyone,
this morning I got an email from bioconductor.
The message:
According to the "Build/check report" for BioC 3.0,
the flowCHIC package has the following problem(s):
ERROR for 'R CMD check' on zin1.
The error I get is the following:
Error in callGeneric() :
'callGeneric' with a prim
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