On Wed, May 13, 2015 at 1:48 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote:
> the original workflow idea was exactly that it should go beyond a single > package. > My question here was not about workflow intent. It was about the vehicle for maintaining a workflow. Some are created as documents only, and a package is generated from the document; others are authored as packages and the workflow document is a vignette of the enclosing package (I think). Making a valid package is a bit more involved than making a computable workflow document from which a package is autogenerated. > Having domain specific cores might be controversial since we often have > multiple packages competing in the same domain. To some extent the > GenomicRanges/Biostring/etc/etc is a special case of this, where "everyone" > is using these packages. To me it sounds too much like an official > endorsement of a specific combination of packages. With workflows, all one > is saying is that "you can use package A,B,C to accomplish tasks 1,2,3"; > there is no official endorsement of a "winner". I think this is worth > thinking about: I think the project does benefit from multiple attempts at > achieving the same result and the resulting competition it creates. > Fair point. Competing workflows are also quite possible. There's a tension between simplicity for the user and complexity/cacophony induced by allowing multiple solutions in the system. I think the user gains more from the complex system even if it is a bit harder to "use". > > > Best, > Kasper > > On Tue, May 12, 2015 at 11:26 PM, Vincent Carey < > st...@channing.harvard.edu> wrote: > >> Agreed that the workflow vehicle should get more attention. Do all >> workflows correspond to packages? >> >> On Tue, May 12, 2015 at 7:31 PM, Michael Lawrence < >> lawrence.mich...@gene.com >> > wrote: >> >> > I like the idea of having multiple, domain-specific cores. Those could >> also >> > serve as a vehicle for high-level documentation, including the workflows >> > but also more "cheat-sheet" and/or cookbook-style documentation. Rafa >> has >> > brought this up on the phone calls. >> > >> > >> > On Tue, May 12, 2015 at 4:10 PM, Hervé Pagès <hpa...@fredhutch.org> >> wrote: >> > >> > > SummarizedExperiment was just an example. I agree it can be a >> > > little challenging for end users to know where to find a particular >> > > functionality but I'm not sure about using "meta" packages to address >> > > that. At least I feel we should probably avoid creating new "meta" >> > > packages out of the blue, with arbitrary limits and possibly endless >> > > discussions about what exactly goes in them. Also I don't think there >> > > is a single "core" but rather several domain-specific cores. >> > > >> > > What about using the existing workflow packages instead? >> > > A workflow package (like the variants package here >> > > http://bioconductor.org/help/workflows/variants/) >> > > covers a specific domain and loading it should load the "core" >> > > for that domain. Plus the user gets a great vignette as a bonus >> > > to get started so it's not just an empty shell. >> > > >> > > There are probably some shortcomings with workflow packages >> > > that would need to be addressed before they can serve as >> > > convenient "meta" packages though e.g. they're treated too >> > > differently from other BioC packages (e.g. they're not available >> > > via biocLite() and don't show up under the biocViews tree here >> > > http://bioconductor.org/packages/release/BiocViews.html). >> > > Nothing that seems impossible to address though... >> > > >> > > H. >> > > >> > > >> > > On 05/12/2015 03:22 PM, Michael Lawrence wrote: >> > > >> > >> It's more general than SummarizedExperiment. I think people would >> > >> appreciate a simple way to load the core, without having to remember, >> > >> for example, that VCF reading is in VariantAnnotation. >> > >> >> > >> On Mon, May 11, 2015 at 9:51 PM, Hervé Pagès <hpa...@fredhutch.org >> > >> <mailto:hpa...@fredhutch.org>> wrote: >> > >> >> > >> Hi Michael, >> > >> >> > >> On 05/11/2015 05:35 PM, Michael Lawrence wrote: >> > >> >> > >> Splitting stuff into different packages is good for >> modularity, >> > >> but >> > >> tough on the mind of the user. What about having some sort of >> > >> "meta" >> > >> package that simply loads the core infrastructure packages? >> > Named >> > >> something simple like "Genomics" or "GenomicsCore". >> > >> >> > >> >> > >> Don't know if we need this. For example, for all the >> > >> SummarizedExperiment use cases I ran into, the end-user generally >> > >> only needs to load the corresponding high-level package (DESeq2, >> > >> VariantAnnotation, minfi, GenomicAlignments, etc...) and that >> takes >> > >> care of loading all the low-level infrastructure packages. >> > >> >> > >> H. >> > >> >> > >> >> > >> On Mon, May 11, 2015 at 5:10 PM, Hervé Pagès >> > >> <hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> >> > >> <mailto:hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>>> >> > >> wrote: >> > >> >> > >> Hi Tim, >> > >> >> > >> The SummarizedExperiment class is being replaced with >> the >> > >> RangedSummarizedExperiment class from the new >> > >> SummarizedExperiment >> > >> package. This is a work-in-progress and the name and >> > internal >> > >> representation of the RangedSummarizedExperiment class >> are >> > >> not >> > >> finalized yet. The main goal for now is to move all the >> > >> SummarizedExperiment stuff from GenomicRanges to its own >> > >> package. >> > >> >> > >> Anyway, metadata() is the replacement for exptData() on >> > >> RangedSummarizedExperiment objects. It's on my list to >> add >> > >> an exptData method for backward compatibility. >> > >> >> > >> Cheers, >> > >> H. >> > >> >> > >> >> > >> On 05/11/2015 04:37 PM, Tim Triche, Jr. wrote: >> > >> >> > >> who determined that breaking this would be a good >> > idea?!? >> > >> >> > >> R> ?SummarizedExperiment >> > >> Help on topic 'SummarizedExperiment' was found in >> the >> > >> following >> > >> packages: >> > >> >> > >> Package Library >> > >> GenomicRanges >> > >> /home/tim/R/x86_64-pc-linux-gnu-library/3.2 >> > >> SummarizedExperiment >> > >> >> > >> /home/tim/R/x86_64-pc-linux-gnu-library/3.2 >> > >> >> > >> R> nrows <- 200; ncols <- 6 >> > >> R> counts <- matrix(runif(nrows * ncols, 1, >> > >> 1e4), nrows) >> > >> R> rowRanges <- GRanges(rep(c("chr1", >> "chr2"), >> > >> c(50, 150)), >> > >> + IRanges(floor(runif(200, >> > >> 1e5, 1e6)), >> > >> width=100), >> > >> + strand=sample(c("+", >> "-"), >> > >> 200, TRUE)) >> > >> R> colData <- >> DataFrame(Treatment=rep(c("ChIP", >> > >> "Input"), 3), >> > >> + >> row.names=LETTERS[1:6]) >> > >> R> sset <- >> > >> >> SummarizedExperiment(assays=SimpleList(counts=counts), >> > >> + rowRanges=rowRanges, >> > >> colData=colData) >> > >> R> sset >> > >> class: RangedSummarizedExperiment >> > >> dim: 200 6 >> > >> metadata(0): >> > >> assays(1): counts >> > >> rownames: NULL >> > >> rowRanges metadata column names(0): >> > >> colnames(6): A B ... E F >> > >> colData names(1): Treatment >> > >> R> assayNames(sset) >> > >> [1] "counts" >> > >> R> assays(sset) <- endoapply(assays(sset), >> > asinh) >> > >> R> head(assay(sset)) >> > >> A B C D E F >> > >> [1,] 6.89 8.81 9.46 9.20 8.88 9.44 >> > >> [2,] 5.07 9.70 4.08 7.47 8.91 5.64 >> > >> [3,] 9.88 9.84 8.95 9.07 9.86 9.06 >> > >> [4,] 9.89 8.88 8.92 8.05 8.46 9.51 >> > >> [5,] 9.75 8.48 4.73 9.86 8.43 9.86 >> > >> [6,] 9.29 9.13 9.80 9.77 9.50 8.40 >> > >> R> exptData(sset) >> > >> Error in (function (classes, fdef, mtable) : >> > >> unable to find an inherited method for function >> > >> 'exptData' >> > >> for signature >> > >> '"RangedSummarizedExperiment"' >> > >> >> > >> >> > >> >> > >> It's one of those things that's a handy place to put >> > >> data when >> > >> you need to >> > >> carry it around for the same set of people/subjects >> but >> > >> don't >> > >> have a handy >> > >> multidimensional container for it. So it's a bit >> of a >> > >> drag that >> > >> it now >> > >> breaks... >> > >> >> > >> >> > >> Bonus: >> > >> >> > >> R> ?"exptData,SummarizedExperiment-method" >> > >> >> > >> SummarizedExperiment-class package:GenomicRanges >> > R >> > >> Documentation >> > >> >> > >> SummarizedExperiment instances >> > >> >> > >> Description: >> > >> >> > >> The SummarizedExperiment class is a >> matrix-like >> > >> container >> > >> where >> > >> rows represent ranges of interest (as a >> 'GRanges >> > >> or >> > >> GRangesList-class') and columns represent >> > >> samples (with >> > >> sample >> > >> data summarized as a 'DataFrame-class'). A >> > >> 'SummarizedExperiment' >> > >> contains one or more assays, each represented >> > by a >> > >> matrix-like >> > >> object of numeric or other mode. >> > >> >> > >> >> > >> >> > >> >> > >> R> sessionInfo() >> > >> R version 3.2.0 (2015-04-16) >> > >> Platform: x86_64-pc-linux-gnu (64-bit) >> > >> Running under: Ubuntu 15.04 >> > >> >> > >> 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] grid stats4 parallel stats >> graphics >> > >> grDevices datasets >> > >> [8] utils methods base >> > >> >> > >> other attached packages: >> > >> [1] disintegrator_0.4.8 vegan_2.2-1 >> > >> [3] permute_0.8-3 CCAGFA_1.0.4 >> > >> [5] FEM_2.3.0 >> org.Hs.eg.db_3.1.2 >> > >> [7] igraph_0.7.1 corrplot_0.73 >> > >> [9] marray_1.47.0 >> AnnotationDbi_1.31.6 >> > >> [11] MotifDb_1.10.0 PWMEnrich_4.5.0 >> > >> [13] SCAN.UPC_2.10.0 sva_3.15.0 >> > >> [15] genefilter_1.51.0 mgcv_1.8-6 >> > >> [17] nlme_3.1-120 affyio_1.37.0 >> > >> [19] affy_1.47.0 oligo_1.33.0 >> > >> [21] oligoClasses_1.31.0 SRAdb_1.23.0 >> > >> [23] RCurl_1.95-4.6 bitops_1.0-6 >> > >> [25] graph_1.47.0 quadprog_1.5-5 >> > >> [27] mclust_5.0.1 >> > >> ConsensusClusterPlus_1.23.0 >> > >> [29] simulatorZ_1.5.1 CoxBoost_1.4 >> > >> [31] prodlim_1.5.1 rsig_1.0 >> > >> [33] survival_2.38-1 DMRcate_1.5.42 >> > >> [35] matrixStats_0.14.0 rtracklayer_1.29.5 >> > >> [37] Matrix_1.2-0 qvalue_2.1.0 >> > >> [39] impute_1.43.0 DMRcatedata_1.5.0 >> > >> [41] minfi_1.15.3 bumphunter_1.8.0 >> > >> [43] locfit_1.5-9.1 iterators_1.0.7 >> > >> [45] foreach_1.4.2 Biostrings_2.37.2 >> > >> [47] XVector_0.9.1 >> > >> SummarizedExperiment_0.1.1 >> > >> [49] GenomicRanges_1.21.9 GenomeInfoDb_1.5.2 >> > >> [51] IRanges_2.3.8 S4Vectors_0.7.2 >> > >> [53] lattice_0.20-31 limma_3.25.3 >> > >> [55] ks_1.9.4 rgl_0.95.1247 >> > >> [57] mvtnorm_1.0-2 misc3d_0.8-4 >> > >> [59] KernSmooth_2.23-14 dplyr_0.4.1 >> > >> [61] GEOmetadb_1.29.0 RSQLite_1.0.0 >> > >> [63] DBI_0.3.1 GEOquery_2.35.4 >> > >> [65] Biobase_2.29.1 BiocGenerics_0.15.0 >> > >> [67] bigrquery_0.1.0.9000 >> BiocInstaller_1.19.5 >> > >> [69] magrittr_1.5 gtools_3.4.2 >> > >> >> > >> loaded via a namespace (and not attached): >> > >> [1] Hmisc_3.16-0 plyr_1.8.2 >> > >> splines_3.2.0 >> > >> [4] BiocParallel_1.3.9 ggplot2_1.0.1 >> > >> digest_0.6.8 >> > >> [7] SuppDists_1.1-9.1 gdata_2.16.1 >> > >> GMD_0.3.3 >> > >> [10] checkmate_1.5.2 BBmisc_1.9 >> > >> cluster_2.0.1 >> > >> [13] annotate_1.47.0 siggenes_1.43.0 >> > >> colorspace_1.2-6 >> > >> [16] tcltk_3.2.0 registry_0.2 >> > >> gtable_0.1.2 >> > >> [19] zlibbioc_1.15.0 RGCCA_2.0 >> > >> evd_2.3-0 >> > >> [22] scales_0.2.4 futile.options_1.0.0 >> > >> pheatmap_1.0.2 >> > >> [25] rngtools_1.2.4 Rcpp_0.11.6 >> > >> xtable_1.7-4 >> > >> [28] foreign_0.8-63 bit_1.1-12 >> > >> preprocessCore_1.31.0 >> > >> [31] Formula_1.2-1 lava_1.4.0 >> > >> glmnet_2.0-2 >> > >> [34] httr_0.6.1 gplots_2.17.0 >> > >> RColorBrewer_1.1-2 >> > >> [37] acepack_1.3-3.3 ff_2.2-13 >> > >> reshape_0.8.5 >> > >> [40] XML_3.98-1.1 nnet_7.3-9 >> > >> reshape2_1.4.1 >> > >> [43] munsell_0.4.2 tools_3.2.0 >> > >> stringr_1.0.0 >> > >> [46] bootstrap_2015.2 beanplot_1.2 >> > >> caTools_1.17.1 >> > >> [49] doRNG_1.6 nor1mix_1.2-0 >> > >> biomaRt_2.25.1 >> > >> [52] stringi_0.4-1 superpc_1.09 >> > >> futile.logger_1.4.1 >> > >> [55] GenomicFeatures_1.21.2 survcomp_1.19.0 >> > >> gbm_2.1.1 >> > >> [58] survivalROC_1.0.3 multtest_2.25.0 >> > >> R6_2.0.1 >> > >> [61] latticeExtra_0.6-26 gridExtra_0.9.1 >> > >> affxparser_1.41.2 >> > >> [64] codetools_0.2-11 lambda.r_1.1.7 >> > >> seqLogo_1.35.0 >> > >> [67] MASS_7.3-40 assertthat_0.1 >> > >> proto_0.3-10 >> > >> [70] pkgmaker_0.22 GenomicAlignments_1.5.8 >> > >> Rsamtools_1.21.4 >> > >> [73] mixOmics_5.0-4 rpart_4.1-9 >> > >> base64_1.1 >> > >> [76] illuminaio_0.11.0 rmeta_2.16 >> > >> >> > >> >> > >> >> > >> >> > >> Statistics is the grammar of science. >> > >> Karl Pearson >> > >> <http://en.wikipedia.org/wiki/The_Grammar_of_Science> >> > >> >> > >> [[alternative HTML version deleted]] >> > >> >> > >> _______________________________________________ >> > >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> > >> <mailto:Bioc-devel@r-project.org <mailto: >> > 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 <mailto: >> hpa...@fredhutch.org> >> > >> <mailto:hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>> >> > >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> > >> <tel:%28206%29%20667-5791> >> > >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> > >> <tel:%28206%29%20667-1319> >> > >> >> > >> >> > >> _______________________________________________ >> > >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> > >> <mailto:Bioc-devel@r-project.org >> > >> <mailto: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 <mailto:hpa...@fredhutch.org> >> > >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> > >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> > >> >> > >> >> > >> >> > > -- >> > > 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 >> > > >> > >> > [[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 >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
