[Bioc-devel] exptData(SummarizedExperiment)
Vincent Carey
stvjc at channing.harvard.edu
Wed May 13 05:26:58 CEST 2015
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
>
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