[Bioc-devel] exptData(SummarizedExperiment)
Tim Triche, Jr.
tim.triche at gmail.com
Tue May 12 01:37:47 CEST 2015
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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