[Bioc-sig-seq] psetdiff on GRangesLists Error

[Dario Strbenac]

Hello,

I'm encountering some strange behaviour. If I do psetdiff with 2 GRangesLists that I have, it gives an error, but if I split the GRangesLists into 2 parts I can't get the error to happen. Any ideas ?

>     length(gene.juncts)
[1] 36693
>     length(gene.exons)
[1] 36693
>     intronics <- psetdiff(gene.juncts, gene.exons)

Error in gaps(union(gaps(x, end = seqlengths), y, ignore.strand = ignore.strand),  : 
  error in evaluating the argument 'x' in selecting a method for function 'gaps': Error in sort.list(runValue(x), na.last = na.last, decreasing = decreasing,  : 
  too large a range of values in 'x'
>     intronics <- psetdiff(gene.juncts[1:20000], gene.exons[1:20000])
>     intronics <- psetdiff(gene.juncts[20001:length(gene.juncts)], gene.exons[20001:length(gene.exons)])
>

To help with troubleshooting, the two GRangesLists are available for download.
http://129.94.136.7/file_dump/dario/testPsetDiff.RData (3.7 MB)

> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.4.1 GenomicRanges_1.4.6   IRanges_1.10.4       

loaded via a namespace (and not attached):
[1] Biobase_2.11.10     biomaRt_2.7.2       Biostrings_2.19.18 
[4] BSgenome_1.19.6     DBI_0.2-5           RCurl_1.6-1        
[7] RSQLite_0.9-4       rtracklayer_1.11.12 XML_3.4-0

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia