[BioC] rtracklayer: Problems running vignette
James W. MacDonald
jmacdon at med.umich.edu
Fri Jun 5 14:57:35 CEST 2009
Michael Lawrence wrote:
>
>
> On Thu, Jun 4, 2009 at 7:03 AM, James W. MacDonald
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>> wrote:
>
> Hi Michael,
>
> I get the same results as Simon. In fact, if I source() the vignette
> code and then run some of the chunks that are set to eval=false, I
> get errors:
>
> > source("c:/R-2.9.0/library/rtracklayer/doc/rtracklayer.R")
> Loading required package: hgu133plus2.db
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: Biostrings
> Loading required package: IRanges
> [snip]
>
> > session <- browserSession("UCSC")
> > track(session, "targets") <- targetTrack
> > targetTrack
> RangedData: 3063 ranges by 3 columns
> columns(3): strand name target
> sequences(23): chr1 chr10 chr11 chr12 chr13 ... chr7 chr8 chr9 chrX
> > view <- browserView(session, range(targetTrack)*-10, pack="targets")
> Error in validObject(x) :
> invalid class "IRanges" object: the widths must be non-NA integers
> In addition: Warning message:
> In numeric2integer(value) : NAs introduced by coercion
> Error in ucscForm(range) :
> error in evaluating the argument 'object' in selecting a method for
> function 'ucscForm'
> > view <- browserView(session, range(subTargetTrack) * -10,pack =
> "targets")
> Error in resolveTrackIndex(x, i) : Unknown tracks:targets
>
> If I export targetTrack as a bedfile and upload to UCSC I get no
> errors and can view the track without problems.
>
>
> I'm kind of at a loss here. I have your same sessionInfo on my machine
> (fresh R install, everything via biocLite) and yet it seems to work just
> fine. What's your curl version? Mine is 7.19.4.
I am on Windows, and am using the binary from BioC, so the curl version
is whatever you guys are using to build the package with. I assume it is
relatively new?
Jim
>
> Michael
>
>
>
> On another subject, you might consider replacing the plot of the
> cpneTrack in the vignette with a .png rather than a .pdf. Trying to
> scroll through the vignette is a real drag when you get to that plot.
>
>
> Yes, good idea.
>
>
>
>
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods
> [7] base
>
> other attached packages:
> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11
> [2] BSgenome_1.12.2
> [3] rtracklayer_1.4.0
> [4] RCurl_0.97-3
> [5] bitops_1.0-4.1
> [6] org.Hs.eg.db_2.2.11
> [7] microRNA_1.2.0
> [8] Rlibstree_0.3-2
> [9] Biostrings_2.12.4
> [10] IRanges_1.2.2
> [11] genefilter_1.24.2
> [12] humanStemCell_0.2.0
> [13] hgu133plus2.db_2.2.11
> [14] RSQLite_0.7-1
> [15] DBI_0.2-4
> [16] AnnotationDbi_1.6.0
> [17] affy_1.22.0
> [18] Biobase_2.4.1
> [19] limma_2.18.1
> [20] biomaRt_2.0.0
>
>
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0 annotate_1.22.0 preprocessCore_1.6.0
> [4] splines_2.9.0 survival_2.35-4 tools_2.9.0
> [7] XML_2.3-0 xtable_1.5-5
>
> Best,
>
> Jim
>
>
>
> Michael Lawrence wrote:
>
> On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders at ebi.ac.uk
> <mailto:anders at ebi.ac.uk>> wrote:
>
> Hi Michael,
>
> I've just tried to use rtracklayer, following your vignette,
> and ran into
> two problems.
>
>
> 1. I cannot add any tracks to a session.
>
> I entered the code in the vignette to produce the "targets"
> track and
> exported it as "targets.bed". To make things easier to
> follow, let's say, I
> start from there with a fresh R session:
>
> library(rtracklayer)
>
> # Import the data
> targets <- import("targets.bed")
> # targets is now a RangedData object with 3052 ranges and
> # sequence names chr1 chr10 chr11 chr12 ...
>
> # Create a session
> session <- browserSession("UCSC")
>
> # Add the 'targets' track to the session:
> track(session, "MYTRACK") <- targets
>
> Is this last command correct? It does not produce an error,
> but it does not
> seem to do anything, either. If I list all the tracks in the
> session with
> trackNames(session)
> I get a list of 196 UCSC standard tracks, but "MYTRACK" is
> not mentioned.
>
> How do I correctly add a track?
>
>
> Well, I can say that this works for me. I need to look into
> parsing the
> error messages returned by UCSC. You can always try uploading
> to UCSC
> manually to see what went wrong. I know that back in December
> the BED output
> was mishandling the score values.
>
>
>
> 2. There is some mangling happening with the chromosome names.
>
> The man page for 'browserView' suggests to try:
>
> browserView(session, GenomicRanges(20000, 50000, "chr2"))
>
> Doing this asks my web browser to open the following URL:
>
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314
> <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314>
>
> Note that it says "chrchr2", i.e., a superfluous "chr" got
> prefixed to the
> sequence name. Obviously, the UCSC page cannot deal with
> this and one gets
> an error message displayed by JavaScript that "chrchr2" is
> not known.
>
> I run into the same problem if I follow the vignette's code
> to demonstrate
> 'browserView'.
>
> If I try
> browserView(session, GenomicRanges(20000, 50000, "2"))
> I get the range chr2:20000-50000 correctly displayed in my
> web browser.
> There is, however, still now sight of "MYTRACK".
>
> What's going wrong here?
>
>
> Thanks for pointing this out. I've fixed this for version 1.5.3.
>
> Michael
>
>
>
> sessionInfo()
>
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] rtracklayer_1.4.0 RCurl_0.94-1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0
> IRanges_1.2.0
> [5] XML_2.3-0
>
>
> Cheers
> Simon
>
>
> +---
> | Dr. Simon Anders, Dipl. Phys.
> | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
> | office phone +44-1223-492680, mobile phone +44-7505-841692
> | preferred (permanent) e-mail: sanders at fs.tum.de
> <mailto:sanders at fs.tum.de>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>
>
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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