Rtracklayer and track/table names
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@gustavo-fernandez-bayon-5300
Last seen 8.2 years ago
Spain
Hi everybody. I am currently using rtracklayer a lot, but I am experiencing some problems with the names of the trackas and tables. For example, I wanted to query the NKI Lads track, which is a hg18 liftover available from the UCSC browser. I do the following: > s <- browserSession() > genome(s) <- 'hg19' > tn <- trackNames(s) > tn[grep('lamin', tn)] NKI Nuc Lamina... "laminB1Super" > query <- ucscTableQuery(s, track='laminB1Super') Error en normArgTrack(track, trackids) : Unknown track: laminB1Super This has happened to me several times, specially when the track names contain the 'Super' string. I guess this represents the concept of supertracks that I have previously seen in the browser. With other tracks, Broad Histone for example, I experienced the same problem but was able to find a workaround by inspecting the table names in the browser, and then discovering there were actual tracks and tables corresponding to them. Problem is, I cannot do that with the NKI Lads track. Is there any way to circumvent this problem? What are the 'Super' track names intended for? Any hint or advice will be appreciated (a lot) Regards, Gus PS: I nearly forgot my sessionInfo(). Here it is: > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 [4] BiocGenerics_0.4.0 ggbio_1.6.6 ggplot2_0.9.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 [4] Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5 [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1 [10] DBI_0.2-5 dichromat_2.0-0 digest_0.6.2 [13] GenomicFeatures_1.10.1 grid_2.15.2 gridExtra_0.9.1 [16] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1 [19] lattice_0.20-13 MASS_7.3-23 munsell_0.4 [22] parallel_2.15.2 plyr_1.8 proto_0.3-10 [25] RColorBrewer_1.0-5 RCurl_1.95-3 reshape2_1.2.2 [28] Rsamtools_1.10.2 RSQLite_0.11.2 scales_0.2.3 [31] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 [34] VariantAnnotation_1.4.7 XML_3.95-0.1 zlibbioc_1.4.0
rtracklayer rtracklayer • 1.1k views
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@gustavo-fernandez-bayon-5300
Last seen 8.2 years ago
Spain
Hi again. I have just found a way to overcome my previous problem. I am posting it here, in case somebody needs it. Went to the UCSC Table Browser, and found the corresponding track and table name in the selection boxes. Track I was searching was 'NKI LADs (Tig3)' and table name was 'laminB1Lads'. But, the question remains, i.e., do the 'super' track names have any utility? And, if the track names returned by trackNames(session) do not have any relationship with the real names, should we skip that step and just obtain the correct names manually? Regards, Gus On 05/02/13 09:38, Gustavo Fern?ndez Bay?n wrote: > Hi everybody. > > I am currently using rtracklayer a lot, but I am experiencing some > problems with the names of the trackas and tables. For example, I > wanted to query the NKI Lads track, which is a hg18 liftover available > from the UCSC browser. I do the following: > > > s <- browserSession() > > genome(s) <- 'hg19' > > tn <- trackNames(s) > > tn[grep('lamin', tn)] > NKI Nuc Lamina... > "laminB1Super" > > query <- ucscTableQuery(s, track='laminB1Super') > Error en normArgTrack(track, trackids) : Unknown track: laminB1Super > > This has happened to me several times, specially when the track names > contain the 'Super' string. I guess this represents the concept of > supertracks that I have previously seen in the browser. With other > tracks, Broad Histone for example, I experienced the same problem but > was able to find a workaround by inspecting the table names in the > browser, and then discovering there were actual tracks and tables > corresponding to them. Problem is, I cannot do that with the NKI Lads > track. > > Is there any way to circumvent this problem? What are the 'Super' > track names intended for? > > Any hint or advice will be appreciated (a lot) > > Regards, > Gus > > PS: I nearly forgot my sessionInfo(). Here it is: > > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C > [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 > [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 > [4] BiocGenerics_0.4.0 ggbio_1.6.6 ggplot2_0.9.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 > [4] Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5 > [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1 > [10] DBI_0.2-5 dichromat_2.0-0 digest_0.6.2 > [13] GenomicFeatures_1.10.1 grid_2.15.2 gridExtra_0.9.1 > [16] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1 > [19] lattice_0.20-13 MASS_7.3-23 munsell_0.4 > [22] parallel_2.15.2 plyr_1.8 proto_0.3-10 > [25] RColorBrewer_1.0-5 RCurl_1.95-3 reshape2_1.2.2 > [28] Rsamtools_1.10.2 RSQLite_0.11.2 scales_0.2.3 > [31] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 > [34] VariantAnnotation_1.4.7 XML_3.95-0.1 zlibbioc_1.4.0 > >
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The problem is that you are trying to use an identifier from the genome browser interface with the table browser. Those do not always match. Instead, just create a query object and query it for the track names: > s <- browserSession() > query <- ucscTableQuery(s) > tn <- trackNames(query) > tn[grep('lamin', tn)] LaminB1 (Tig3) NKI LADs (Tig3) "laminB1" "laminB1Lads" It should be possible for rtracklayer to create a UCSCTableQuery object directly, without creating a browser session first, but currently the API is centered around the genome browser session, with other interfaces being initialized from it. This reflects the origin of the package as a genome visualization tool. These days, it's mostly used as a data access tool. Michael On Tue, Feb 5, 2013 at 12:52 AM, Gustavo Fernández Bayón <gbayon@gmail.com>wrote: > Hi again. > > I have just found a way to overcome my previous problem. I am posting it > here, in case somebody needs it. Went to the UCSC Table Browser, and found > the corresponding track and table name in the selection boxes. Track I was > searching was 'NKI LADs (Tig3)' and table name was 'laminB1Lads'. > > But, the question remains, i.e., do the 'super' track names have any > utility? And, if the track names returned by trackNames(session) do not > have any relationship with the real names, should we skip that step and > just obtain the correct names manually? > > Regards, > Gus > > > > On 05/02/13 09:38, Gustavo Fernández Bayón wrote: > >> Hi everybody. >> >> I am currently using rtracklayer a lot, but I am experiencing some >> problems with the names of the trackas and tables. For example, I wanted to >> query the NKI Lads track, which is a hg18 liftover available from the UCSC >> browser. I do the following: >> >> > s <- browserSession() >> > genome(s) <- 'hg19' >> > tn <- trackNames(s) >> > tn[grep('lamin', tn)] >> NKI Nuc Lamina... >> "laminB1Super" >> > query <- ucscTableQuery(s, track='laminB1Super') >> Error en normArgTrack(track, trackids) : Unknown track: laminB1Super >> >> This has happened to me several times, specially when the track names >> contain the 'Super' string. I guess this represents the concept of >> supertracks that I have previously seen in the browser. With other tracks, >> Broad Histone for example, I experienced the same problem but was able to >> find a workaround by inspecting the table names in the browser, and then >> discovering there were actual tracks and tables corresponding to them. >> Problem is, I cannot do that with the NKI Lads track. >> >> Is there any way to circumvent this problem? What are the 'Super' track >> names intended for? >> >> Any hint or advice will be appreciated (a lot) >> >> Regards, >> Gus >> >> PS: I nearly forgot my sessionInfo(). Here it is: >> >> > sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 >> [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 >> [4] BiocGenerics_0.4.0 ggbio_1.6.6 ggplot2_0.9.3 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 >> [4] Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5 >> [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1 >> [10] DBI_0.2-5 dichromat_2.0-0 digest_0.6.2 >> [13] GenomicFeatures_1.10.1 grid_2.15.2 gridExtra_0.9.1 >> [16] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1 >> [19] lattice_0.20-13 MASS_7.3-23 munsell_0.4 >> [22] parallel_2.15.2 plyr_1.8 proto_0.3-10 >> [25] RColorBrewer_1.0-5 RCurl_1.95-3 reshape2_1.2.2 >> [28] Rsamtools_1.10.2 RSQLite_0.11.2 scales_0.2.3 >> [31] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 >> [34] VariantAnnotation_1.4.7 XML_3.95-0.1 zlibbioc_1.4.0 >> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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