This makes sense.
Thanks for the fast answer and for this really nice package.
Best,
Laurent
2013/10/9 Michael Lawrence <lawrence.mich...@gene.com>
> It's not feasible to download an entire genome's worth of mappability data
> using rtracklayer and the underlying table browser interface. UCSC has
> limits in place that truncate the response. rtracklayer has little way of
> knowing whether the user is requesting too many records. Just download the
> mappability as a bigwig file via FTP and query that with rtracklayer,
> instead.
>
>
> On Wed, Oct 9, 2013 at 9:45 AM, laurent jacob <laurent.ja...@gmail.com>wrote:
>
>> Hi everyone,
>>
>> I'm trying to use the ucscTableQuery function from the rtracklayer
>> package to download a mapability table from the ucsc genome browser.
>>
>> Everything works fine if I restrict the query to a small range, but I get
>> an error message when querying the entire genome (at the moment where I
>> convert the UCSCTableQuery using track()):
>>
>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
>> na.strings, :
>> scan() expected 'an integer', got 'section'
>>
>> Here is a short example:
>>
>> ---------
>> library(rtracklayer)
>> mySession = browserSession('UCSC')
>> genome(mySession) <- 'hg19'
>> range <- GRanges('chr1', IRanges(start=10013, end=10021))
>> query.range <- ucscTableQuery(mySession, track='wgEncodeMapability',
>> range=range,
>> table='wgEncodeCrgMapabilityAlign100mer')
>>
>> query.full <- ucscTableQuery(mySession, track='wgEncodeMapability',
>> range='hg19',
>> table='wgEncodeCrgMapabilityAlign100mer')
>>
>> ## This works
>> track(query.range)
>> ## This fails
>> track(query.full)
>> -----------
>>
>> Do you have any idea of what may cause this error?
>>
>> My sessionInfo() and traceback() of the error are given below.
>>
>> Best,
>>
>> Laurent
>>
>> --------------------------------
>> > sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] rtracklayer_1.21.12 GenomicRanges_1.13.51 XVector_0.1.4
>> [4] IRanges_1.19.38 BiocGenerics_0.7.5
>>
>> loaded via a namespace (and not attached):
>> [1] Biostrings_2.29.19 bitops_1.0-6 BSgenome_1.29.1
>> RCurl_1.95-4.1
>> [5] Rsamtools_1.13.48 stats4_3.0.2 tools_3.0.2
>> XML_3.98-1.1
>> [9] zlibbioc_1.7.0
>> ---------------------------------
>>
>> ---------------------------------
>> > traceback()
>> 34: 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)
>> 33: read.table(con, colClasses = bedClasses, as.is = TRUE, na.strings =
>> ".",
>> comment.char = "")
>> 32: DataFrame(read.table(con, colClasses = bedClasses, as.is = TRUE,
>> na.strings = ".", comment.char = ""))
>> 31: .local(con, format, text, ...)
>> 30: import(FileForFormat(con, format), ...)
>> 29: import(FileForFormat(con, format), ...)
>> 28: import(text = lines, format = "bedGraph", genome = genome,
>> asRangedData = asRangedData,
>> which = which, seqinfo = seqinfo)
>> 27: import(text = lines, format = "bedGraph", genome = genome,
>> asRangedData = asRangedData,
>> which = which, seqinfo = seqinfo)
>> 26: .local(con, format, text, ...)
>> 25: import(FileForFormat(con, format), ...)
>> 24: import(FileForFormat(con, format), ...)
>> 23: import(format = subformat, text = text, asRangedData = asRangedData,
>> genome = genome, ...)
>> 22: import(format = subformat, text = text, asRangedData = asRangedData,
>> genome = genome, ...)
>> 21: FUN(1L[[1L]], ...)
>> 20: lapply(seq_along(trackLines), makeTrackSet)
>> 19: lapply(seq_along(trackLines), makeTrackSet)
>> 18: .local(con, format, text, ...)
>> 17: import(FileForFormat(con, format), ...)
>> 16: import(FileForFormat(con, format), ...)
>> 15: import(con, "ucsc", ...)
>> 14: import(con, "ucsc", ...)
>> 13: import.ucsc(resource(con), subformat = subformat, ...)
>> 12: import.ucsc(resource(con), subformat = subformat, ...)
>> 11: .local(con, ...)
>> 10: import.ucsc(initialize(file, resource = con), drop = TRUE, trackLine
>> = FALSE,
>> genome = genome, asRangedData = asRangedData, which = which,
>> seqinfo = seqinfo, ...)
>> 9: import.ucsc(initialize(file, resource = con), drop = TRUE, trackLine =
>> FALSE,
>> genome = genome, asRangedData = asRangedData, which = which,
>> seqinfo = seqinfo, ...)
>> 8: .local(con, format, text, ...)
>> 7: import(FileForFormat(con, format), ...)
>> 6: import(FileForFormat(con, format), ...)
>> 5: import(text = output, format = format, asRangedData = asRangedData,
>> seqinfo = seqinfo(range(object)))
>> 4: import(text = output, format = format, asRangedData = asRangedData,
>> seqinfo = seqinfo(range(object)))
>> 3: .local(object, ...)
>> 2: track(query.full)
>> 1: track(query.full)
>> --------------------------------------
>>
>>
>> --
>> Laurent Jacob
>> Laboratoire de Biométrie et Biologie Évolutive
>> CNRS/Université Lyon 1
>> http://cbio.ensmp.fr/~ljacob
>>
>
>
--
Laurent Jacob
Laboratoire de Biométrie et Biologie Évolutive
CNRS/Université Lyon 1
http://cbio.ensmp.fr/~ljacob
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