On Mon, Oct 13, 2014 at 9:44 PM, Hervé Pagès wrote:
> Hi,
>
> On 10/11/2014 02:25 PM, Vincent Carey wrote:
>
>> On Sat, Oct 11, 2014 at 5:17 PM, Michael Lawrence <
>> lawrence.mich...@gene.com
>>
>>> wrote:
>>>
>>
>> But what it would do exactly?
>>>
>>> Probably would want to be able to extract
Hi,
On 10/11/2014 02:25 PM, Vincent Carey wrote:
On Sat, Oct 11, 2014 at 5:17 PM, Michael Lawrence
wrote:
But what it would do exactly?
Probably would want to be able to extract a gene list from a TxDb, then
extract the desired type of structure from the TxDb.
Not too bad right now, but it
On Sat, Oct 11, 2014 at 5:17 PM, Michael Lawrence wrote:
> But what it would do exactly?
>
> Probably would want to be able to extract a gene list from a TxDb, then
> extract the desired type of structure from the TxDb.
>
> Not too bad right now, but it would be nice to leverage the identifier
>
But what it would do exactly?
Probably would want to be able to extract a gene list from a TxDb, then
extract the desired type of structure from the TxDb.
Not too bad right now, but it would be nice to leverage the identifier type
information on the gene list object.
Currently:
tx <- transcripts
On 10/11/2014 08:41 AM, Vincent Carey wrote:
Is there anything on the order of as([GeneSet], "GRanges") around?
no, I don't think so; obviously of use and following a common theme. Martin
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker wrote:
Sean and Vincent,
The goal of what we are doing
Is there anything on the order of as([GeneSet], "GRanges") around?
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker wrote:
> 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-w
On Mon, Sep 22, 2014 at 10:17 AM, Cook, Malcolm wrote:
> Hi,
>
> >
> https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw
> >
> >shows some modifications to [ that allow subsetting of SE by
> >gene or pathway name
>
> Without reading the code, do you intend that SE[i,j
Hi,
>https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw
>
>shows some modifications to [ that allow subsetting of SE by
>gene or pathway name
Without reading the code, do you intend that SE[i,j] will , if i is provided
as vector of string, will subset those rows wh
Sounds very nice. Anything for the impending release?
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker wrote:
> 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 l
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
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
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
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