I am sure there are better responses to come, but here are a few initial comments.
On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson <mviter...@gmail.com> wrote: > Dear all, > > SummarizedExperiment and matrixStats both contain a method/function called > rowRanges one operates on a SummarizedExperiment-object the other on a > matrix. matrixStats is required by SummarizedExperiment, or a package it is > depending on, so rowRanges is masked when loading SummarizedExperiment. > > I thought a function/method is called depended on the type of the object; > There are at least two interpretations of this. If a function that is an S3 generic is called on an entity whose class corresponds to an existing method, that method will be invoked. If a function that is an S4 generic is called with (a sequence of) arguments corresponding to a method with signature equivalent to the sequence of classes of the arguments, that method will be invoked. In matrixStats, rowRanges is just a first level function, and will be invoked directly on anything that is passed -- e.g., rowRanges(4) is just an error, when matrixStats alone is loaded. matrix or SummarizedExperiment-object, such that functions/methods with the > same name can coexist. However, this doesn't seems to work for rowRanges. > The only way to access rowRanges from matrixStats when SummarizedExperiment > is already loaded is using the double colon operator > matrixStats::rowRanges. Is this intentional or is there a other way to > solve this? > > Regards, > Maarten > > Here is a small example showing the issue: > > > library(SummarizedExperiment) > Loading required package: matrixStats > matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for > help. > Attaching package: ‘matrixStats’ > Attaching package: ‘SummarizedExperiment’ > The following object is masked from ‘package:matrixStats’: > rowRanges > > nrows <- 200; ncols <- 6 > > counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) > > rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)), > + IRanges(floor(runif(200, 1e5, 1e6)), width=100), > + strand=sample(c("+", "-"), 200, TRUE), > + feature_id=sprintf("ID%03d", 1:200)) > > colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3), > + row.names=LETTERS[1:6]) > > rse <- SummarizedExperiment(assays=SimpleList(counts=counts), > + rowRanges=rowRanges, colData=colData) > > > > rowRanges(rse) > GRanges object with 200 ranges and 1 metadata column: > seqnames ranges strand | feature_id > <Rle> <IRanges> <Rle> | <character> > [1] chr1 [858613, 858712] - | ID001 > > > > rowRanges(counts) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ‘rowRanges’ for signature > ‘"matrix"’ > > > > library(matrixStats) ##it is already loading so this doesn't alter the > Actually in this case matrixStats is loaded and attached. Sometimes the difference is significant. > search path > > > > rowRanges(rse) > GRanges object with 200 ranges and 1 metadata column: > seqnames ranges strand | feature_id > <Rle> <IRanges> <Rle> | <character> > [1] chr1 [858613, 858712] - | ID001 > > rowRanges(counts) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ‘rowRanges’ for signature > ‘"matrix"’ > So -- we got a warning when there was a collision in namespaces, when SummarizedExperiment was attached, and an indication that rowRanges is an S4 generic when we encountered the error. When should we introduce the method setMethod("rowRanges", "matrix", function(x, ...) matrixStats::rowRanges(x, ...)) that would foster the behavior I think you are looking for? > > > head(matrixStats::rowRanges(counts)) > [,1] [,2] > [1,] 51.27791 9350.048 > [2,] 1417.41010 8272.040 > > sessionInfo() > R Under development (unstable) (2016-08-25 r71150) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 14.04.5 LTS > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] SummarizedExperiment_1.5.7 DelayedArray_0.1.7 > [3] matrixStats_0.51.0 Biobase_2.35.1 > [5] GenomicRanges_1.27.23 GenomeInfoDb_1.11.10 > [7] IRanges_2.9.19 S4Vectors_0.13.15 > [9] BiocGenerics_0.21.3 > > loaded via a namespace (and not attached): > [1] lattice_0.20-34 bitops_1.0-6 grid_3.4.0 > [4] zlibbioc_1.21.0 XVector_0.15.2 Matrix_1.2-8 > [7] RCurl_1.95-4.8 GenomeInfoDbData_0.99.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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