[BioC] subsetting SummarizedExperiments - a proposal (or a hack?)
Steve Lianoglou
lianoglou.steve at gene.com
Fri Feb 14 19:22:21 CET 2014
Cool, indeed ... thanks Martin!
-steve
On Thu, Feb 13, 2014 at 11:15 PM, Cook, Malcolm <MEC at stowers.org> wrote:
> Martin,
>
> I may have run out of Hoorays, but your commit today implementing subset for SummarizedExperiments is surely deserving of a few "WooHoos" and a "Yowsah!".
>
> So....
>
> WooHoo WooHoo and a big ol' Yowsah!
>
> Thanks!
>
> ~ malcolm_cook at stowers.org
> ________________________________
> From: Cook, Malcolm
> Sent: Thursday, February 13, 2014 12:20 PM
> To: 'Michael Lawrence'; 'Martin Morgan'
> Cc: 'bioconductor at r-project.org'
> Subject: RE: [BioC] subsetting SummarizedExperiments - a proposal (or a hack?)
>
> Michael,
>
> Just to say, "Hooray" on your response to this thread, and especially more recent activity, where I see:
>
>
> 1) your discussion on R-devel re 'getting environment from "top" promise: http://r.789695.n4.nabble.com/getting-environment-from-quot-top-quot-promise-td4685138.html#none
>
> 2) your commit last night in service of allowing interfaces to GRanges (change log copied below)
>
> What nice syntactic sugar you are serving us. And what lurking dragons and self-inflicted gunshot wounds to the foot your are saving me.
>
> I look forward to the next release!
>
> Did I say "Hooray!"
>
> Hooray!
>
> ~Malcolm
>
> Revision: 86351
> Author: m.lawrence
> Date: a day ago
> Paths:
> Modified
>
> /trunk/madman/Rpacks/IRanges/R/Vector-class.R<https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges/R/Vector-class.R>
>
> Modified
>
> /trunk/madman/Rpacks/IRanges/NAMESPACE<https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges/NAMESPACE>
>
> Modified
>
> /trunk/madman/Rpacks/IRanges/R/List-class.R<https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges/R/List-class.R>
>
> Modified
>
> /trunk/madman/Rpacks/IRanges/DESCRIPTION<https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges/DESCRIPTION>
>
> generalize eval() to Vectors, add as.env,Vector that forms an
> environment by querying the Vector for fixedColumnNames() and the
> mcols(). fixedColumnNames() returns an empty vector of names by
> default, but e.g. GenomicRanges can use it to provide start, end,
> etc. Change subset() and with() to call eval directly on the
> Vector. Now we can do subset(gr, seqnames=="chr2" & score > 15).
>
>
> From: Michael Lawrence [mailto:lawrence.michael at gene.com]
> Sent: Saturday, February 08, 2014 7:55 AM
> To: Martin Morgan
> Cc: Cook, Malcolm; bioconductor at r-project.org
> Subject: Re: [BioC] subsetting SummarizedExperiments - a proposal (or a hack?)
>
>
>
> On Wed, Feb 5, 2014 at 5:54 PM, Martin Morgan <mtmorgan at fhcrc.org<mailto:mtmorgan at fhcrc.org>> wrote:
> Hi Malcom --
>
> On 02/05/2014 02:11 PM, Cook, Malcolm wrote:
>> Martin,
>>
>> Google says: 'Your search - "subset.SummarizedExperiment" - did not match any documents.'
> If it had existed, it would have been an S4 method revealed by
>
> library(GenomicAlignments) # library(GenomicRanges) in release
> showMethods("subset")
> method?"subset,SummarizedExperiment"
> ?"subset,SummarizedExperiment-method"
>
> with tab completion available on the last two after getting through "subset". Google would have found "subset,SummarizedExperiment-method" (if it existed) but Google and tab completion with ? would have failed (though the latter in perhaps a suggestive way by showing alternate tab completions) when a relevant method is defined on a contained class. But yes, a method does not exist.
>
>>
>> So I offer the below for your consideration, along with a few examples and a quick benchmark comparison with using the more explicit `[` extraction operator.
>>
>>
>>
>> subset.SummarizedExperiment<-function(x
>> ,rowSubset=TRUE
>> ,colSubset=TRUE
>> ,assaySubset=TRUE
>> ,drop=FALSE
>> ,provenanceTrack=FALSE
>> ,...) {
>> ## PURPOSE: implement subsetting of SummarizedExperiments,
>> ## allowing expressions in terms of:
>> ##
>> ## + the GRanges (and its mcols meta-data) held in rowData
>> ## + the experimental meta-data held in the colData DataFrame
>> ## + the names of the assays
>> x<-x[
>> ##eval(as.expression(substitute(row)),mcols(rowData(x)),.GlobalEnv)
>> eval(as.expression(substitute(rowSubset)),as.data.frame(rowData(x)),.GlobalEnv)
>> ,eval(as.expression(substitute(colSubset)),colData(x),.GlobalEnv)
>> ,drop=drop,...]
>> if (! identical(TRUE,assaySubset)) assays(x)<-assays(x)[assaySubset]
>> if(provenanceTrack) {
>> exptData(x)$rowSubset<-c(exptData(x)$rowSubset,as.character(substitute(rowSubset)))
>> exptData(x)$colSubset<-c(exptData(x)$colSubset,as.character(substitute(colSubset)))
>> }
>> x
>> }
>> attr(subset,'ex')<-function() {
>> example(SummarizedExperiment)
>> assays(se1)$a2<-assays(se1)$counts*2
>> assays(se1)$a3<-assays(se1)$counts*3
>> benchmark(replications=100
>> ,se1.ss1<-se1[start(rowData(se1))==344757,se1$Treatment=='ChIP']
>> ,se1.ss2<-subset(se1,start==344757,Treatment=='ChIP')
>> )
>> stopifnot(identical(assays(se1.ss1),assays(se1.ss2)))
>> se1.ss3<-subset(se1,strand=='+',Treatment=='ChIP',c('a2','a3'))
>> stopifnot(identical(c('a2','a3'),names(assays(se1.ss3))))
>> }
>>
>>
>> The rbenchmarks shows the cost of overhead in this contrived minimal example. YMMV:
>>
>> test replications elapsed relative user.self sys.self user.child sys.child
>> 3 c("a2", "a3") 100 0.001 1 0.001 0.000 0 0
>> 1 se1.ss1 <- se1[start(rowData(se1)) == 344757, se1$Treatment == "ChIP"] 100 3.113 3113 3.111 0.001 0 0
>> 2 se1.ss2 <- subset(se1, start == 344757, Treatment == "ChIP") 100 3.486 3486 3.486 0.000 0 0
>>
>> Is all this in the spirit of things as you see it? It sure makes my use of SE "scan" (erhm, like poetry;)
> My own problem with subset() is that the context of the call is hard to get correct. So your subset with this
>
> f <- function(x) {
> id <- 697568
> subset(x, start==id)
> }
>
> fails
>
>> f(se1)
> Error in x[eval(as.expression(substitute(rowSubset)), as.data.frame(rowData(x)), :
> error in evaluating the argument 'i' in selecting a method for function '[': Error in eval(expr, envir, enclos) : object 'id' not found
>
> and this fails (does not select the value of id set in f()) silently
>
>> id <- 387456
>> start(f(se1))
> [1] 387456
>
> I think I might have solved this problem with a simple solution. The promise knows the expression and the environment in which to evaluate it. Since we have no problem getting the expression with substitute(), why not get the environment, too?
> Just added this to IRanges and it seems to work:
>
> SEXP top_prenv(SEXP nm, SEXP env)
> {
> SEXP promise = findVar(nm, env);
> while(TYPEOF(promise) == PROMSXP) {
> env = PRENV(promise);
> promise = PREXPR(promise);
> }
> return env;
> }
> Let's see if we can break it.
>
>
> Other R idioms are similarly dangerous even for data.frame using base::subset.data.frame as illustrated here
>
> http://stackoverflow.com/questions/9860090/in-r-why-is-better-than-subset
>
> in the high-voted answer.
>
> But maybe I shouldn't stand between users, guns, and feet?
>
> A couple of small SummarizedExperiment things in your code ...
>
> start(se1) == start(rowData(se1))
>
> and likewise for other functions in the GRanges 'API'. Also it turns out that it is expensive in the (current) implementation of SummarizedExperiment to associated dimnames with returned assay() or assays(), so it is much faster to
>
> assays(x) <- assays(x, withDimnames=FALSE)[assaySubset]
>
> (dimnames get stored on the rowData and colData rather than redundantly on (each of the) assays, although this is probably a false (space) economy). The combination of GRanges API and expensive assay() / assays() can help save one from unintended inefficiencies, e.g., dimnames(se1) rather than dimnames(assay(se1)).
>
> Martin
>
>>
>> if you like, I also have castLong and castWide functions to reshape a (subsetted) SE as a data.table for use in ggplot and friends.
>>
>> You like?
>>
>> Cheers,
>>
>> ~Malcolm
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793<tel:%28206%29%20667-2793>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org<mailto:Bioconductor at r-project.org>
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Steve Lianoglou
Computational Biologist
Genentech
More information about the Bioconductor
mailing list