Dear Bioc-sig-sequencing, I would like to learn about the rtracklayer package by working thru its vignette using code in rtracklayer.R
I have tried using both the stable and developer versions of R. There appears to be an error when using the stable version. The developer version comes to a point where I don't know how to proceed. A short description for each attempt follows. P.Terry [email protected] ########################################################################## 1. Stable version. Chunk 19 produces error message: > subTargetTrack <- targetTrack[1,] # get first feature > view <- browserView(session, range(subTargetTrack) * -10, + pack = "targets") Error in resolveTrackIndex(x, i) : Unknown tracks:targets > If skip forward to chunk 22 (2.2.4 A shortcut) > browseGenome(subTargetTrack) A genome browser session of class 'UCSCSession' with 1 views and 206 tracks > Produces new Foxfire browser page at ucsc browser, but with a window (box) near top of the page with the error message: Error(s): * Sorry, couldn't locate chrchr1 in genome database My sessionInfo() is: > sessionInfo() R version 2.9.2 (2009-08-24) x86_64-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 [4] org.Hs.eg.db_2.2.11 microRNA_1.2.0 Rlibstree_0.3-2 [7] Biostrings_2.12.8 IRanges_1.2.3 limma_2.18.3 [10] genefilter_1.24.2 humanStemCell_0.2.2 hgu133plus2.db_2.2.11 [13] RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.6.1 [16] Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 BSgenome_1.12.3 splines_2.9.2 survival_2.35-5 [5] tools_2.9.2 XML_2.5-1 xtable_1.5-5 > 2. Developer version (R-49517) At chunk 14: > track(session, "targets") <- targetTrack Called from: FUN(X[[1L]], ...) Browse[1]> My question is what to do at this point? Ctl^C won't return to R prompt ? My sessionInfo() is > sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-01 r49517) x86_64-unknown-linux-gnu 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=C 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] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.5.12 RCurl_1.2-0 bitops_1.0-4.1 [4] microRNA_1.3.1 Rlibstree_0.3-2 Biostrings_2.13.36 [7] IRanges_1.3.66 limma_2.19.4 genefilter_1.25.7 [10] humanStemCell_0.2.3 hgu133plus2.db_2.3.4 org.Hs.eg.db_2.3.4 [13] RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.7.11 [16] Biobase_2.5.6 loaded via a namespace (and not attached): [1] annotate_1.23.1 BSgenome_1.13.11 splines_2.10.0 survival_2.35-5 [5] tools_2.10.0 XML_2.6-0 xtable_1.5-5 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
