Perfect, thanks much! Also for the GRanges tip. I foresee a convenience for SummarizedExperiment-derived objects' colData arising from this (e.g. rsem.se$mutan\t)
*He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* Benjamin Franklin, Poor Richard's Almanack<http://archive.org/details/poorrichardsalma00franrich> On Wed, Nov 13, 2013 at 9:25 AM, Martin Morgan <mtmor...@fhcrc.org> wrote: > On 11/13/2013 09:17 AM, Tim Triche, Jr. wrote: > >> This seems like what I'm looking for, but it doesn't do what I'd expect: >> >> R> rc.options(ipck=TRUE) >> R> rc.options()$ipck >> [1] TRUE >> R> require(Biostr\t >> # nothing happens >> >> Should I be using one of the intermediate/undocumented functions to grab a >> list of possible completions? >> > > should be rc.settings(ipck=TRUE) > > Tab completion can be pretty useful to customize for class developers, for > instance library(GenomicRanges); .DollarNames.GenomicRanges is what enables > tab completion on the metadata column names > > > gr = GRanges("chr1", IRanges(1, 10), foo=1, bar=2) > > gr$f<tab> > > Martin > > >> Thanks, >> >> --t >> >> >> R> sessionInfo() >> R Under development (unstable) (2013-11-11 r64202) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> 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] parallel stats graphics grDevices datasets utils methods >> [8] base >> >> other attached packages: >> [1] Matrix_1.1-0 >> [2] frma_1.15.1 >> [3] BSgenome.Hsapiens.UCSC.hg19_1.3.19 >> [4] BSgenome_1.31.6 >> [5] Biostrings_2.31.1 >> [6] Homo.sapiens_1.1.1 >> [7] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 >> [8] org.Hs.eg.db_2.10.1 >> [9] GO.db_2.10.1 >> [10] RSQLite_0.11.4 >> [11] DBI_0.2-7 >> [12] OrganismDbi_1.5.0 >> [13] GenomicFeatures_1.15.2 >> [14] AnnotationDbi_1.25.3 >> [15] Biobase_2.23.2 >> [16] chromophobe_0.79 >> [17] fastcluster_1.1.11 >> [18] pheatmap_0.7.7 >> [19] ggplot2_0.9.3.1 >> [20] reshape2_1.2.2 >> [21] GenomicRanges_1.15.9 >> [22] XVector_0.3.1 >> [23] IRanges_1.21.8 >> [24] BiocGenerics_0.9.0 >> [25] BiocInstaller_1.13.2 >> [26] gtools_3.1.1 >> [27] devtools_1.3 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.35.0 affy_1.41.1 affyio_1.31.0 >> >> [4] biomaRt_2.19.1 bit_1.1-10 bitops_1.0-6 >> >> [7] codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0 >> >> [10] digest_0.6.3 evaluate_0.5.1 ff_2.2-12 >> >> [13] foreach_1.4.1 GenomicAlignments_0.99.2 graph_1.41.1 >> >> [16] grid_3.1.0 gtable_0.1.2 httr_0.2 >> >> [19] iterators_1.0.6 labeling_0.2 lattice_0.20-24 >> >> [22] MASS_7.3-29 matrixStats_0.8.12 memoise_0.1 >> >> [25] munsell_0.4.2 oligo_1.27.0 oligoClasses_1.25.1 >> >> [28] plyr_1.8 preprocessCore_1.25.0 proto_0.3-10 >> >> [31] R.methodsS3_1.5.2 RBGL_1.39.1 RColorBrewer_1.0-5 >> >> [34] RCurl_1.95-4.1 Rsamtools_1.15.7 rtracklayer_1.23.3 >> >> [37] scales_0.2.3 splines_3.1.0 stats4_3.1.0 >> >> [40] stringr_0.6.2 tools_3.1.0 whisker_0.3-2 >> >> [43] XML_3.98-1.1 zlibbioc_1.9.0 >> >> >> *He that would live in peace and at ease, * >> *Must not speak all he knows, nor judge all he sees.* >> >> Benjamin Franklin, Poor Richard's >> Almanack<http://archive.org/details/poorrichardsalma00franrich> >> >> >> On Wed, Nov 13, 2013 at 8:43 AM, Deepayan Sarkar >> <deepayan.sar...@gmail.com>wrote: >> >> On Wed, Nov 13, 2013 at 10:06 PM, Tim Triche, Jr. <tim.tri...@gmail.com> >>> wrote: >>> >>>> How hard would this be to set up (e.g. using a mechanism like >>>> AnnotationHub's)? >>>> >>>> I'm really lazy and wondering if the time spent writing a little package >>>> might be recovered when I want to load a BSgenome or SNPlocs (or...) >>>> package this way. >>>> >>>> Plus if the mechanism could involve caching, maybe that could work for >>>> biocLite too. >>>> >>>> Just a thought. How much trouble am I looking at and what should I >>>> watch >>>> out for? >>>> >>> >>> Set >>> >>> rc.options(ipck = TRUE) >>> >>> and try again. Is this what you are looking for? >>> >>> -Deepayan >>> >>> thanks, >>>> >>>> --t >>>> >>>> >>>> *He that would live in peace and at ease, * >>>> *Must not speak all he knows, nor judge all he sees.* >>>> >>>> Benjamin Franklin, Poor Richard's >>>> Almanack<http://archive.org/details/poorrichardsalma00franrich> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
