[Bioc-devel] exptData(SummarizedExperiment)
Michael Lawrence
lawrence.michael at gene.com
Wed May 13 01:31:25 CEST 2015
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
>
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