[BioC] Rtracklayer and track/table names
Gustavo Fernández Bayón
gbayon at gmail.com
Tue Feb 5 09:38:13 CET 2013
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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