Martin, Thank you for the detailed explanation. I will check it out soon. By the way, I really like the bioconductor class you gave last week. The materials were well organized and truly helpful for me. Thank you. Sean ________________________________________ From: Martin Morgan [mtmorgan@fhcrc.org] Sent: Sunday, February 17, 2013 8:45 PM To: Sean Wang [guest] Cc: bioconductor at r-project.org; Wang, Sean; gmapR Maintainer Subject: Re: [BioC] where is exonsOnTP53Genome defined 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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