[BioC] ChIPpeakAnno/IRanges - getAllPeakSequence(data, upstream = 25, downstream = 25, genome=Mmusculus)

[Zhu, Lihua (Julie)]

Silvia,

I reproduced the same error by trying to fetch a sequence from coordinates
that are greater than the reference chromosome length. So I suspect that
your dataset contains coordinates beyond the ranges of the reference
chromosome. Please let me know whether this is the culprit. Thanks!

Best regards,

Julie 


On 1/14/13 11:56 AM, "Lihua Julie Zhu" <julie.zhu at umassmed.edu> wrote:

> Silvia,
> 
> I understand that you cannot send the whole dataset. Could you please just
> send me the chromosome,strand, start and end information for the row that
> caused the problem so that I can try to reproduce the error? Also, could you
> please update ChIPpeakAnno to 2.6  and see if that resolves the problem
> http://www.bioconductor.org/packages/2.11/bioc/html/ChIPpeakAnno.html? Thanks!
> 
> Best regards,
> 
> Julie
> 
> 
> On 1/14/13 11:23 AM, "Silvia von der Heyde" <silvia.heyde at gmail.com> wrote:
> 
> Hello,
> 
> thanks for the quick response. Unfortunately I cannot supply the data, but the
> session info is the following:
> 
> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices datasets  utils     methods
> [8] base
> 
> other attached packages:
>  [1] coda_0.15-2                         rGADEM_2.4.0
>  [3] seqLogo_1.22.0                      cureos_0.3
>  [5] multicore_0.1-7                     BayesPeak_1.8.0
>  [7] org.Mm.eg.db_2.7.1                  rtracklayer_1.16.3
>  [9] ShortRead_1.14.4                    latticeExtra_0.6-24
> [11] RColorBrewer_1.0-5                  Rsamtools_1.8.6
> [13] lattice_0.20-10                     BSgenome.Mmusculus.UCSC.mm9_1.3.17
> [15] BiocInstaller_1.4.9                 ChIPpeakAnno_2.4.0
> [17] limma_3.12.3                        org.Hs.eg.db_2.7.1
> [19] GO.db_2.7.1                         RSQLite_0.11.2
> [21] DBI_0.2-5                           AnnotationDbi_1.18.4
> [23] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.24.0
> [25] GenomicRanges_1.8.13                Biostrings_2.24.1
> [27] IRanges_1.14.4                      multtest_2.12.0
> [29] Biobase_2.16.0                      biomaRt_2.12.0
> [31] BiocGenerics_0.2.0                  gplots_2.11.0
> [33] MASS_7.3-22                         KernSmooth_2.23-8
> [35] caTools_1.13                        bitops_1.0-4.1
> [37] gdata_2.12.0                        gtools_2.7.0
> 
> loaded via a namespace (and not attached):
> [1] hwriter_1.3      RCurl_1.95-1.1   splines_2.15.0   stats4_2.15.0
> [5] survival_2.36-14 tools_2.15.0     XML_3.95-0.1     zlibbioc_1.2.0
> 
> I ithink it should be related to IRanges package...
> My output.1 data object (used as input when the problem occurs) has the
> following start ranges and width
>  range(output.1$ranges at start)
> [1]   2999950 194976340
> range(output.1$ranges at width)
> [1]  101 3551
> 
> Many thanks!
> 
> 2013/1/14 Zhu, Lihua (Julie) <Julie.Zhu at umassmed.edu>
> Dear Silvia,
> 
> Could you please send me the test data and code that resulted in this error
> message? Please also send me your session information as well.  Thanks!
> 
> Best regards,
> 
> Julie
> 
> 
> 
> On 1/14/13 6:33 AM, "Silvia von der Heyde" <silvia.heyde at gmail.com
> <http://silvia.heyde@gmail.com> > wrote:
> 
> Hello!
> 
> I have a problem with the function mentioned above (should be solve_user_SEW
> invoked by getAllPeakSequence) and I hope you can help me.
> I get an error:
> "in .Call2("solve_user_SEW", refwidths, start, end, width,
> translate.negative.coord,  : solving row 1: 'allow.nonnarrowing' is FALSE and
> the supplied start (130043477) is > refwidth + 1"
> I've already read in some mailing lists that this is known but I did not find
> any solution for that.
> 
> Many thanks in advance,
> Silvia
> 
> 
> 
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> 
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