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
>
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