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
