hi, Is there a way that I can change the names of the assays slot of a SummarizedExperiment, without making a new copy of the data contained within? Assume I get an SE which has already been constructed, but no names on the assays() SimpleList.
thanks, Mike > library(GenomicRanges) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1291106 69 1710298 91.4 1590760 85.0 Vcells 1178619 9 1925843 14.7 1724123 13.2 > m <- matrix(1:2e7, ncol=10) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1291111 69.0 1967602 105.1 1590760 85.0 Vcells 11178604 85.3 22482701 171.6 21178631 161.6 # made a ~75 Mb matrix > colnames(m) <- letters[1:10] > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1291149 69.0 1967602 105.1 1590760 85.0 Vcells 11178679 85.3 22482701 171.6 21179851 161.6 > se <- SummarizedExperiment(m) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1302603 69.6 1967602 105.1 1623929 86.8 Vcells 12189777 93.1 22482701 171.6 21179851 161.6 # so far no copying > names(assays(se)) <- "counts" > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1303174 69.6 1967602 105.1 1623929 86.8 Vcells 22190847 169.4 23686836 180.8 22203423 169.4 # last step made a copy > sessionInfo() R Under development (unstable) (2014-05-07 r65539) Platform: x86_64-apple-darwin12.5.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.17.12 GenomeInfoDb_1.1.3 IRanges_1.99.13 [4] S4Vectors_0.0.6 BiocGenerics_0.11.2 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 stats4_3.2.0 XVector_0.5.6 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel