[Bioc-devel] exptData(SummarizedExperiment)
Tim Triche, Jr.
tim.triche at gmail.com
Wed May 13 19:53:48 CEST 2015
I personally don't care as long as I have a cubbyhole for unstructured data
and the name of that cubbyhole doesn't change every few weeks
hence the patch that I sent about 12 hours after complaining :-)
Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
On Wed, May 13, 2015 at 10:48 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:
> the original workflow idea was exactly that it should go beyond a single
> package.
>
> 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.
>
> Best,
> Kasper
>
> On Tue, May 12, 2015 at 11:26 PM, Vincent Carey <
> stvjc at 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.michael at 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 <hpages at 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 <hpages at fredhutch.org
> > > >> <mailto:hpages at 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
> > > >> <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
> > > >> <mailto:hpages at fredhutch.org <mailto:hpages at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
> > > >> <mailto:Bioc-devel at r-project.org <mailto:
> > > Bioc-devel at 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: hpages at fredhutch.org <mailto:
> > hpages at fredhutch.org>
> > > >> <mailto:hpages at fredhutch.org <mailto:hpages at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
> > > >> <mailto:Bioc-devel at r-project.org
> > > >> <mailto:Bioc-devel at 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: hpages at fredhutch.org <mailto:hpages at 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: hpages at fredhutch.org
> > > > Phone: (206) 667-5791
> > > > Fax: (206) 667-1319
> > > >
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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