Thanks, Hervé! On 26/01/2016, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Pete, > > On 01/25/2016 12:32 PM, Peter Hickey wrote: >> The Matrix virtual class in the Matrix package seems to mostly work as >> an assays element in a SummarizedExperiment. This is especially useful >> for data that can be efficiently represented as a sparse matrix, e.g., >> using the dgCMatrix class. >> >> My understanding is that this works because the (concrete subclasses >> of) Matrix implement the necessary basic S4 methods to form a basic, >> matrix-like API. However, there are a couple of edge cases that I'm >> hoping it might be possible to smoothen out. Ideally, I'd love if this >> could work for any class that implements a minimal matrix-like API >> (I'm currently experimenting with such a class) and not just for the >> Matrix virtual class and its concrete subclasses. From reading the >> SummarizedExperiment code, it looks like the minimal methods required >> for an element of a (concrete subclass of) Assays object would be dim, >> dimnames, [, [<-, rbind, cbind, length. I suppose that if any >> additional methods are added for the Assays virtual class (e.g., I >> have an almost-complete combine,SummarizedExperiment-method that calls >> a combine,Assays-method) then these matrix-like objects must also have >> such methods defined to ensure relatively straightforward inheritance. >> >> Here are a couple of instances where a matrix and a Matrix behave >> (understandably) differently but where it would be nice if it "just >> worked". There may well be others, but I'd be interested to know >> whether this is worth further pursuing. >> >> library(SummarizedExperiment) >> library(Matrix) >> m <- matrix(1:10, ncol = 2) >> m2 <- Matrix(m) >> >> # SummarizedExperiment constructor has specialised matrix method. >> se <- SummarizedExperiment(m) >> # This won't work because there is no Matrix specialisation >> se2 <- SummarizedExperiment(m2) >> # But can get around this by wrapping the Matrix in a SimpleList to defer >> to >> # the SummarizedExperiment,SimpleList-method >> se2 <- SummarizedExperiment(SimpleList(m2)) > > Note that wrapping the Matrix in an ordinary list also works. > >> # I guess the only way around this is to write a SummarizedExperiment >> method >> # for every matrix-like class, which might be too much overhead for the >> # SummarizedExperiment package to maintain. Perhaps there is another >> solution, >> # e.g., try wrapping the input in a call to SimpleList if no method found >> and >> # then deferring to the SimpleList method? Could be too messy to be worth >> it ... > > The method for matrix already does this wrapping into a SimpleList > object and then defers to the method for SimpleList method. I just > replaced the current method for matrix by a method for ANY that does > exactly the same thing. With this change, SummarizedExperiment() takes > any matrix-like object. > >> >> # assay<- dispatches on value (which must be a matrix) >> assay(se) <- assay(se) >> # Won't work because there is no Matrix specialisation >> assay(se2) <- assay(se2) >> # But using assays() does work >> assays(se2)[[1]] <- assays(se2)[[1]] >> # Could value be dropped from the assay<- signatuare and the object >> validated >> # during/following the consequent call to assays<-? > > That makes a lot of sense. Having the assay() setter dispatch on 'x', > 'i', and 'value' has no real benefit. Dispatching on 'x' and 'i' is > enough and allows the assay() setter to take any matrix-like object as > long as the resulting SummarizedExperiment object is valid. > > These 2 changes are in SummarizedExperiment 1.1.17. > > Thanks for the suggestions, > H. > >> >> Cheers, >> Pete >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 >
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