Hi Mark,

I was not planning on porting the fix to the released version, as it's not
that critical. A new Bioc release is coming soon anyway.

As for the devel version, I'm guessing this is more to your liking:

> session <- browserSession("UCSC")
> q2 <- ucscTableQuery(session, "all_mrna")
> q2
Get track 'all_mrna' within hg18:*:*-*

That is, you are probably not interested in the (default) chrX but the
entire genome. I keep going back and forth on the logic for deriving the
ranges. I made the change based on the reasoning that one will be working
through a session, with one or more views, and end up at a region of
interest. As the query is constructed from the session, the user would
expect the default query range to be that of the session. In fact, this is
the behavior of the UCSC table browser.

To get what you need, you'll want to specify the range when constructing the
query, e.g:

> q2 <- ucscTableQuery(session, "all_mrna", GenomicRanges(genome = "hg18"))

To get the entire genome's worth of data. I just tweaked the logic to make
this work in version 1.5.20. Btw, you don't need the genome<- call at the
beginning, just do it at query construction time.

Michael

On Sun, Oct 4, 2009 at 3:41 PM, Mark Robinson <mrobinson@wehi.edu.au> wrote:

> Hi Michael.
>
> It looks like I'm still getting some unusual behaviour with 1.5.19 (2.10)
> ... and am unsuccessful with the mrna table on 1.4.1 (2.9).
>
> I'm sending the output for both versions below.  It seems 1.5.19 is only
> gathering results for a small region on chrX and 1.4.1 doesn't accept the
> "all_mrna" table.  I'm using fairly old versions of R 2.9 and 2.10, but I'd
> guess that that is not the issue.
>
> Any suggestions?
>
> Thanks,
> Mark
>
>
> [1.4.1 -- 2.9]
> ---------------------------------
> > library(rtracklayer)
> Loading required package: RCurl
> Loading required package: bitops
> > session <- browserSession("UCSC")
> > genome(session) <- "hg18"
> > q1 <- ucscTableQuery(session, "refGene")
> > q1
> Get track 'refGene' within hg18:*:*-*
> > refGene <- getTable(q1)
> > q2 <- ucscTableQuery(session, "all_mrna")
> Error in normArgTrack(x, track) : Unknown track: all_mrna
> > sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-apple-darwin8.11.1
>
> locale:
> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.4.1 RCurl_0.98-1      bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.4.1     Biostrings_2.12.9 BSgenome_1.12.3   IRanges_1.2.3
> [5] XML_2.6-0
> ---------------------------------
>
>
>
> [1.5.19 -- 2.10]
> ---------------------------------
> > library(rtracklayer)
> Loading required package: RCurl
> Loading required package: bitops
> > session <- browserSession("UCSC")
> > genome(session) <- "hg18"
> > q1 <- ucscTableQuery(session, "refGene")
> > q1
> Get track 'refGene' within hg18:chrX:151073054-151383976
> > refGene <- getTable(q1)
> > q2 <- ucscTableQuery(session, "all_mrna")
> > q2
> Get track 'all_mrna' within hg18:chrX:151073054-151383976
> > mrna <- getTable(q2)
> > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-05-22 r48594)
> i386-apple-darwin8.11.1
>
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.5.19 RCurl_0.98-1       bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.5.8      Biostrings_2.13.48 BSgenome_1.13.16   IRanges_1.3.87
> [5] XML_2.6-0
> ---------------------------------
>
> On 3-Oct-09, at 11:10 AM, Michael Lawrence wrote:
>
>
>>
>> On Thu, Oct 1, 2009 at 11:47 PM, Mark Robinson <mrobinson@wehi.edu.au>
>> wrote:
>> Hello BioC list.
>>
>> I've encountered a small problem when trying to download some tracks from
>> UCSC with rtracklayer.  Specifically, I'm trying to get the "mrna" table.
>>  The example below works great for the "refGene" table, but gives an error
>> for the "mrna" table.
>>
>> Any suggestions?
>>
>>
>> Looked into this and found that the table browser has a slightly different
>> set of tracks from the browser itself. I added a trackNames method (version
>> 1.5.19) on the UCSCTableQuery, so that it's possible to know which tracks
>> are available.
>>
>> From that, you'll see that 'mrna' needs to be 'all_mrna'.
>>
>> Michael
>>
>> Thanks,
>> Mark
>>
>> > library(rtracklayer)
>> Loading required package: RCurl
>> Loading required package: bitops
>> > session <- browserSession("UCSC")
>> > genome(session) <- "hg18"
>> > options(stringsAsFactors=FALSE)
>> > q1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272,
>> 198064461, "chr3"))
>> > tab1 <- getTable(q1)
>> > head(tab1[,1:5])
>>  bin      name chrom strand   txStart
>> 1 2094 NM_198565  chr3      + 197851052
>> 2  261 NM_032898  chr3      - 197917544
>> 3 2095 NM_017861  chr3      + 197923642
>> 4 2095 NM_002577  chr3      + 197951124
>> > q2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, 198064461,
>> "chr3"))
>> > tab2 <- getTable(q2)
>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>>  :
>>  line 1 did not have 2 elements
>> > traceback()
>> 5: scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
>>      nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE,
>>      fill = fill, strip.white = strip.white, blank.lines.skip =
>> blank.lines.skip,
>>      multi.line = FALSE, comment.char = comment.char, allowEscapes =
>> allowEscapes,
>>      flush = flush, encoding = encoding)
>> 4: read.table(f, sep = "\t", header = TRUE)
>> 3: .local(object, ...)
>> 2: getTable(q2)
>> 1: getTable(q2)
>> > sessionInfo()
>> R version 2.9.1 (2009-06-26)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] rtracklayer_1.4.1 RCurl_0.98-1      bitops_1.0-4.1
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.4.1     Biostrings_2.12.8 BSgenome_1.12.3   IRanges_1.2.3
>> [5] XML_2.6-0
>>
>>
>>
>>
>>
>> ---------
>> library(rtracklayer)
>> session <- browserSession("UCSC")
>> genome(session) <- "hg18"
>> options(stringsAsFactors=FALSE)
>> qry1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272,
>> 198064461, "chr3"))
>> tab1 <- getTable(qry1)
>> head(tab1[,1:5])
>> qry2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, 198064461,
>> "chr3"))
>> tab2 <- getTable(qry2)
>> traceback()
>> sessionInfo()
>> ---------
>>
>>
>> ------------------------------
>> Mark Robinson, PhD (Melb)
>> Epigenetics Laboratory, Garvan
>> Bioinformatics Division, WEHI
>> e: m.robinson@garvan.org.au
>> e: mrobinson@wehi.edu.au
>> p: +61 (0)3 9345 2628
>> f: +61 (0)3 9347 0852
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
> ------------------------------
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robinson@garvan.org.au
> e: mrobinson@wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
>
>
>
>
>
>

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