[Bioc-devel] exptData(SummarizedExperiment)
Hervé Pagès
hpages at fredhutch.org
Tue May 12 06:51:53 CEST 2015
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>> 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>
>
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>
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>
> --
> 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>
>
>
> _______________________________________________
> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
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>
>
--
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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