On May 11, 2015, at 5:10 PM, Herv? Pag?s <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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