[BioC] Rtracklayer and track/table names

[Gustavo Fernández Bayón]

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
>
>