Sean and Vincent,
The goal of what we are doing builds off of what Martin has in GSEABase. We
were looking to see how much benefit we can get with something
lighter-weight that lies between indistinguishable character vectors and
the full machinery of GeneSets.
Either way, it seems like formalizi
Hi Martin, Micheal and Vincent,
If I run the following code, with the release version of BiocParallel then it
works (took me some time to actually realize that), but with the development
version I am getting an error shown after the test code below. If I run the
same test with BatchJobs from the
Would be very useful in epivizr. Right now we have a little bit of code
that can be made much more general:
https://github.com/epiviz/epivizr/blob/master/R/register-methods.R#L73
On Sat, Sep 20, 2014 at 5:19 PM, Michael Love
wrote:
> On Sep 20, 2014 2:15 PM, "Martin Morgan" wrote:
> >
> > On 0
On Sep 20, 2014 2:15 PM, "Martin Morgan" wrote:
>
> On 09/20/2014 10:43 AM, Sean Davis wrote:
>>
>> Hi, Vince.
>>
>> Looks like a good start. I'd probably pull all the assays from
>> ExpressionSet into SummarizedExperiment as the default, avoiding data
>> coercion methods that are unnecessarily l
- Original Message -
> From: "Kasper Daniel Hansen"
> To: "Dan Tenenbaum"
> Cc: "bioc-devel"
> Sent: Wednesday, September 17, 2014 5:35:50 PM
> Subject: Re: [Bioc-devel] hedgehog Subversion server upgrade Tuesday 9/30
>
>
> The standard install of subversion on a recent Mac is 1.7.10
On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker wrote:
> Hey all,
>
> We are in the (very) early stages of experimenting with something that
> seems relevant here: classed identifiers. We are using them for
> database/mart queries, but the same concept could be useful for the cases
> you're describi
On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker wrote:
> Hey all,
>
> We are in the (very) early stages of experimenting with something that
> seems relevant here: classed identifiers. We are using them for
> database/mart queries, but the same concept could be useful for the cases
> you're describi
Hey all,
We are in the (very) early stages of experimenting with something that
seems relevant here: classed identifiers. We are using them for
database/mart queries, but the same concept could be useful for the cases
you're describing I think.
E.g.
> mysyms = GeneSymbol(c("BRAF", "BRCA1"))
> my
OK by me to leave [ alone. We could start with subsetByEntrez,
subsetByKEGG, subsetBySymbol, subsetByGOTERM, subsetByGOID.
Utilities to generate GRanges for queries in each of these vocabularies
should, perhaps, be in the OrganismDb space? Once those are in place
no additional infrastructure is
On 09/20/2014 10:43 AM, Sean Davis wrote:
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as it stands, the
assayname argument is not used anyway
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as it stands, the
assayname argument is not used anyway?
Sean
On Sat, Sep 20, 2014 at 10:38 AM,
Agreed with Sean, having tried implementing to "magical" alternative
--t
> On Sep 20, 2014, at 9:31 AM, Sean Davis wrote:
>
> Hi, Vince.
>
> I'm coming a little late to the party, but I agree with Kasper's sentiment
> that the less "magical" approach of using subsetByXXX might be the cleaner
>
Hi, Vince.
I'm coming a little late to the party, but I agree with Kasper's sentiment
that the less "magical" approach of using subsetByXXX might be the cleaner
way to go for the time being.
Sean
On Sat, Sep 20, 2014 at 10:42 AM, Vincent Carey
wrote:
>
> https://github.com/vjcitn/biocMultiAss
https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw
shows some modifications to [ that allow subsetting of SE by
gene or pathway name
it may be premature to work at the [ level. Kasper suggested defining
a suite of subsetBy operations that would accomplish this
i think
do we have a facility for this?
if not, we have
https://github.com/vjcitn/biocMultiAssay/blob/master/R/exs2se.R
https://github.com/vjcitn/biocMultiAssay/blob/master/man/coerce-methods.Rd
it occurred to me that we might want something like this in GenomicRanges
(that's where SummarizedExperiment
15 matches
Mail list logo
