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>
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