[BioC] where is exonsOnTP53Genome defined

[Martin Morgan]

On 02/16/2013 05:59 PM, Sean Wang [guest] wrote:
>
> I saw people used gmapR:::exonsOnTP53Genome("TP53"), but could not find the function exonsOnTP53Genome in the gmapR pdf document.
>
> I tried to issue the following commands in R with gmapR installed to get some help, but none of them works, ?exonsOnTP53Genome, help(exonsOnTP53Genome).
>
> Could anyone give me a hand? I am still new to bioconductor, and would like to pick it up.

Hi Sean -- Bioconductor has a 'release' and a 'development' version. This 
function is in the development version. To use the development version requires 
that you have the 'development' version of R.

If you are using R in a server environment where you do not have administrative 
privileges, it might be easiest to make an 'svn' checkout of the R-devel source, 
and then to build it. This is done with

   cd ~/
   mkdir src
   cd src
   svn co https://svn.r-project.org/R/trunk R-devel
   R-devel/tools/rsync-recommended
   cd ~/
   mkdir -p bin/R-devel
   cd bin/R-devel
   ~/src/R-devel/configure
   make -j

You'll end up with an executable in ~/bin/R-devel/bin/R. After starting it, you can

   source("http://bioconductor.org/biocLite.R")
   biocLite("gmapR")

to get the development version of gmapR and it's dependencies.

Martin


>
>
> Thank you very much.
>
> -Sean
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> 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=C                 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      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] RSQLite_0.11.2
>   [2] DBI_0.2-5
>   [3] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
>   [4] GenomicFeatures_1.10.0
>   [5] AnnotationDbi_1.20.2
>   [6] Biobase_2.18.0
>   [7] gmapR_1.0.0
>   [8] RCurl_1.95-3
>   [9] bitops_1.0-5
> [10] Gviz_1.2.1
> [11] VariantTools_1.0.1
> [12] VariantAnnotation_1.4.9
> [13] Rsamtools_1.10.2
> [14] Biostrings_2.26.2
> [15] GenomicRanges_1.10.5
> [16] IRanges_1.16.4
> [17] BiocGenerics_0.4.0
> [18] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.14.0     biovizBase_1.6.2   BSgenome_1.26.1    cluster_1.14.3
>   [5] colorspace_1.2-0   dichromat_1.2-4    Hmisc_3.10-1       labeling_0.1
>   [9] lattice_0.20-10    munsell_0.4        org.Hs.eg.db_2.8.0 parallel_2.15.2
> [13] plyr_1.7.1         RColorBrewer_1.0-5 rtracklayer_1.18.0 scales_0.2.2
> [17] stats4_2.15.2      stringr_0.6.1      tcltk_2.15.2       tools_2.15.2
> [21] XML_3.95-0.1       zlibbioc_1.4.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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