[Bioc-devel] exptData(SummarizedExperiment)
Vincent Carey
stvjc at channing.harvard.edu
Wed May 13 20:15:15 CEST 2015
On Wed, May 13, 2015 at 1:48 PM, Kasper Daniel Hansen <
kasperdanielhansen at 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 <
> 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
>>
>
>
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