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.ethz.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]]

