[Bioc-sig-seq] psetdiff on GRangesLists Error

[Hervé Pagès]

Hi Dario,

Thanks for catching this one and sorry for the delay, I just "found"
your email today. The problem was that, deep in the code, sort.list()
was used with method="radix", which is a very fast algo, but it does
not support factors with too many levels. In your case the factor
passed to sort.list() had more than 100000 levels which is more than
what method="radix" can handle. Hence the complain:

   too large a range of values in 'x'

This should be fixed in IRanges release (1.10.5) and devel (1.11.20).

Cheers,
H.


On 11-07-20 08:00 PM, Dario Strbenac wrote: the
> 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
>
> _______________________________________________
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> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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