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
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
>
>
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
>>
>>
>>
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