[Bioc-devel] exptData(SummarizedExperiment)
Tim Triche, Jr.
tim.triche at gmail.com
Tue May 12 05:50:26 CEST 2015
I'll write a patch... I'd have to anyway :-)
--t
> On May 11, 2015, at 5:10 PM, Hervé Pagès <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 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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