[Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

On Sat, Oct 11, 2014 at 5:17 PM, Michael Lawrence <lawrence.michael at 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 leverage the identifier
type information on the gene list object.

Currently:
tx <- transcripts(txdb, vals=list(gene_id=genes))

Proposed:
tx <- transcripts(txdb[GeneList])

yes, that makes sense.  i don't go to txdb's as naturally as i should.

On Sat, Oct 11, 2014 at 10:49 AM, Martin Morgan <mtmorgan at fhcrc.org>
wrote:

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.gabe at 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
lighter-weight that lies between indistinguishable character vectors and
the full machinery of GeneSets.

Either way, it seems like formalizing the semantic information is a way
to
do what you want. Furthermore, these classed id objects can be created
automatically when there is contextual information e.g. during queries
to
databases (or db-like objects), and then simply added to metadata
DataFrames and re-used.

~G




On Sat, Sep 20, 2014 at 12:19 PM, Sean Davis <sdavis2 at mail.nih.gov>
wrote:

On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker <becker.gabe at 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
you're describing I think.

E.g.

  mysyms = GeneSymbol(c("BRAF", "BRCA1"))

mysyms

An object of class "GeneSymbol"
[1] "BRAF"  "BRCA1"

yourSE[mysyms, ]

...


  This approach has the flavor of some of the functionality that

Martin put
together for the GSEABase package (EntrezIdentifier, etc.).

Sean

This approach has the benefit of being declarative instead of
heuristic
(people won't be able to accidentally invoke it), while still giving
most
of the convenience I believe you are looking for.

The object classes inherit directly from character, so should "just
work"
most of the time, but as I said it's early days; lots more testing for
functionality and usefulness is needed.

~G


On Sat, Sep 20, 2014 at 11:38 AM, Vincent Carey <
stvjc at channing.harvard.edu>
wrote:

  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 necessary?

On Sat, Sep 20, 2014 at 12:49 PM, Tim Triche, Jr. <

tim.triche at gmail.com>

wrote:

  Agreed with Sean, having tried implementing to "magical" alternative

--t

  On Sep 20, 2014, at 9:31 AM, Sean Davis <sdavis2 at 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 the

cleaner

way to go for the time being.

Sean


On Sat, Sep 20, 2014 at 10:42 AM, Vincent Carey <

stvjc at channing.harvard.edu>

wrote:

  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 we could get something along these lines into the release

without

too much more work.  votes?

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