Benchmarking accessing names of assays in SummarizedExperiment object.

SummarizedExperiment_assay_names.R

library(GenomicRanges)
library(microbenchmark)

nrows <- 2000000; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges(rep(c("chr1", "chr2"), c(0.25 * nrows, 0.75 * nrows)),
                   IRanges(floor(runif(nrows, 1e5, 1e6)), width=100),
                   strand=sample(c("+", "-"), nrows, TRUE))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                     row.names=LETTERS[1:6])
se <- SummarizedExperiment(assays=SimpleList(counts=counts),
                             rowData=rowData, colData=colData)

# The names(se@assays$field("data")) method is based on bsseq::assayNames()
microbenchmark(names(assays(se)), names(assays(se, withDimnames = FALSE)), 
               names(se@assays$field("data")))
# Unit: microseconds
#                                     expr       min        lq        mean     median        uq        max neval
#                        names(assays(se)) 32886.088 35178.628 59443.71397 46207.0240 70830.253 278013.116   100
#  names(assays(se, withDimnames = FALSE))    78.652    87.432   137.93095   123.6345   182.350    363.143   100
#           names(se@assays$field("data"))    46.295    49.646    87.77205    62.0195   124.839    379.928   100

sessionInfo()
# R Under development (unstable) (2014-11-10 r66951)
# Platform: x86_64-apple-darwin10.8.0 (64-bit)
# 
# locale:
# [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
# 
# attached base packages:
# [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] microbenchmark_1.4-2  GenomicRanges_1.19.10 GenomeInfoDb_1.3.7    IRanges_2.1.13        S4Vectors_0.5.6      
# [6] BiocGenerics_0.13.1  
# 
# loaded via a namespace (and not attached):
#  [1] colorspace_1.2-4 digest_0.6.4     ggplot2_1.0.0    grid_3.2.0       gtable_0.1.2     MASS_7.3-35     
#  [7] munsell_0.4.2    plyr_1.8.1       proto_0.3-10     Rcpp_0.11.3      reshape2_1.4     scales_0.2.4    
# [13] stringr_0.6.2    tools_3.2.0      XVector_0.7.2