On 04/01/2015 07:07 AM, Martin Morgan wrote:
On 04/01/2015 05:08 AM, Michael Lawrence wrote:It would be nice if someone from Seattle would weigh in on this.I was hoping to weigh in with 'it's done' but will instead with 'it will be done'.
4-dimensional assays, advisable or otherwise, are available in GenomicRanges 1.19.49. Thanks for your patience, and for the discussion. Martin
A second aspect of Jesper's data that took me a little by surprise and is related to Michael's comment below was that assays() can simultaneously hold arrays of 2, 3, (and 4) dimensions. MartinAlso, we might want to consider an assayMatrix() accessor that always returns an assay in 2D, except, as you suggest, it might be a matrix of multiples (vectors, matrices, etc) by putting dimensions on a list. That way, generic code can at least assume consistent dimensionality, even if the values are complex. I don't really have any use cases though; just seems possibly beneficial in the abstract. On Wed, Apr 1, 2015 at 1:19 AM, Jesper Gådin <jesper.ga...@gmail.com> wrote:Hi Wolfgang and Michael, As Michael says, there is no redundant information in the 4D array I have, and all the values are integers. Of course I can simulate 4D by e.g. creating extra 3D arrays as assays equal to the length of the fourth dimension, but that makes the assay list a mess. It would also require me to write accessor functions that transforms the data into 4D before subsequent calculations (or to use a for loop..). Another option would be to include the 4D as a multiple in the 3D, which would not require a later transformation into 4D. If I understood correct, the array is just a long vector, which is indexed into different dimensions, and so everything in an SE object could as well be written as 2D. But (my belief is that) it is actually convenient to use the properties of dimensions for arrays. So if there is not a problem extending to 4D, I would be extremely grateful if you could take a look at it. :) Regards, Jesper On Tue, Mar 31, 2015 at 2:16 PM, Michael Lawrence < lawrence.mich...@gene.com> wrote:One would need a long-form colData that aligns with the array. But now I realize that's not what Jesper wants to do here, and is not how SE is currently designed. Jesper is using the third (and now fourth) dimension to store an additional dimension of information about the same sample. We already support 3D arrays for this, presumably motivated VCF, where, for example, each sample can have a probability for WT, het, or hom at each position. In that case, all of the values are genotype likelihoods, i.e., they all measure the same thing, so they seem to belong in the same assay. But they're also the same biological "sample". Essentially, we have complex measurements that might be a vector, or for Jesper even a matrix. The important question for interoperability is whether we want there to be a contract that assays are always two dimensions. I guess we've already violated that with VCF. Extending to a fourth is not really hurting anything. On Tue, Mar 31, 2015 at 4:52 AM, Wolfgang Huber <whu...@embl.de> wrote:Hi Michael where would you put the “colData”-style metadata for the 3rd, 4th, … dimensions? As an (ex-)physicists of course I like arrays, and the more dimensions the better, but in practical work I’ve consistently been bitten by the rigidity of such a design choice too early in a process. Wolfgang On 31 Mar 2015, at 13:32, Michael Lawrence <lawrence.mich...@gene.com> wrote: Taken in the abstract, the tidy data argument is one for consistent data structures that enable interoperability, which is what we have with SummarizedExperiment. The "long form" or "tidy" data frame is an effective general representation, but if there is additional structure in your data, why not represent it formally? Given the way R lays out the data in arrays, it should be possible to add that fourth dimension, in an assay array, while still using the colData to annotate that structure. It does not make the data any less "tidy", but it does make it more structured. On Tue, Mar 31, 2015 at 4:14 AM, Wolfgang Huber <whu...@embl.de> wrote:Dear Jesper this is maybe not the answer you want to hear, but stuffing in 4, 5, … dimensions may not be all that useful, as you can always roll out these higher dimensions into the existing third (or even into the second, the SummarizedExperiment columns). There is Hadley’s concept of “tidy data” (see e.g. http://www.jstatsoft.org/v59/i10 ) — a paper that is really worthwhile to read — which implies that the tidy way forward is to stay with 2 (or maybe 3) dimensions in SummarizedExperiment, and to record the information that you’d otherwise stuff into the higher dimensions in the colData covariates. Wolfgang Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany T +49-6221-3878823 wolfgang.hu...@embl.de http://www.huber.embl.deOn 30 Mar 2015, at 12:38, Jesper Gådin <jesper.ga...@gmail.com>wrote:Hi! The SummarizedExperiment class is an extremely powerful container for biological data(thank you!), and all my thinking nowadays is justcirclingaround how to stuff it as effectively as possible. Have been using 3 dimension for a long time, which has been very successful. Now I also have a case for using 4 dimensions. Everything seemed to work as expected until I tried to subset my object, seeexample.library(GenomicRanges) rowRanges <- GRanges( seqnames="chrx", ranges=IRanges(start=1:3,end=4:6), strand="*" ) coldata <- DataFrame(row.names=paste("s",1:3, sep="")) assays <- SimpleList() #two dim assays[["dim2"]] <- array(0,dim=c(3,3)) se <- SummarizedExperiment(assays, rowRanges = rowRanges,colData=coldata)se[1] #works #three dim assays[["dim3"]] <- array(0,dim=c(3,3,3)) se <- SummarizedExperiment(assays, rowRanges = rowRanges,colData=coldata)se[1] #works #four dim assays[["dim4"]] <- array(0,dim=c(3,3,3,3)) se <- SummarizedExperiment(assays, rowRanges = rowRanges,colData=coldata)se[1] #does not work #Error in x[i, , , drop = FALSE] : incorrect number of dimensions This is also the case for rbind and cbind. Would it be appropriate toaskyou to update the SE functions to handle subset, rbind, cbind alsofor 4dimensions? I know the time for next release is very soon, so maybeit isbetter to wait until after April 16. Just let me know your thoughtsaboutit. Jesper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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