Is there anything on the order of as([GeneSet], GRanges) around?
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker becker.g...@gene.com 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
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 becker.g...@gene.com wrote:
Sean and Vincent,
The goal
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 -
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 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
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 where
On Mon, Sep 22, 2014 at 10:17 AM, Cook, Malcolm m...@stowers.org 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
Sounds very nice. Anything for the impending release?
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker becker.g...@gene.com 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
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 st...@channing.harvard.edu
wrote:
Agreed with Sean, having tried implementing to magical alternative
--t
On Sep 20, 2014, at 9:31 AM, Sean Davis sdav...@mail.nih.gov 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
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
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))
mysyms
On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker becker.g...@gene.com 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
On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker becker.g...@gene.com 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
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