[BioC] rtracklayer: Problems running vignette

James W. MacDonald jmacdon at med.umich.edu
Thu Jun 4 16:03:34 CEST 2009 

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.

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.

 > 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> 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
>>
>> 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
>>
>>
>>
>>
> 
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> 
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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

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