[Bioc-devel] exptData(SummarizedExperiment)
Hervé Pagès
hpages at fredhutch.org
Tue May 12 02:10:05 CEST 2015
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
Phone: (206) 667-5791
Fax: (206) 667-1319
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