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
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
