Hello,

I have been using MEDIPS and I happened to get the same error. In my case,
the names of the scaffolds (chromosomes) in the mapping file did not
correspond to the names of the scaffold in the BSgenome (example:
chromosome1 in the BED file vs chr1 in the BSgenome).

Hope it helps.


On Mon, Sep 2, 2013 at 3:46 AM, Yuting Liu [guest]
<guest@bioconductor.org>wrote:

>
> Hi,
> I am following the MEDIPS tutorial to do the Saturation analysis on my own
> data. But I encountered error. Do you have any idea or suggestion about it?
>
> sr=MEDIPS.saturation(file="/home/liuyu1b/PROJECT/Rat_Sar/Mapping
>
> /Q97-k4_filter.bam",BSgenome=BSgenome,uniq=uniq,extend=extend,shif
>
> t=shift,window_size=ws,nit=10,nrit=1,empty_bins=TRUE,rank=FALSE)
> Reading bam alignment Q97-k4_filter.bam
> Total number of imported short reads: 13592073
> Extending reads...
> Creating GRange Object...
> Extract unique regions...
> Number of unique short reads: 13592073
> Loading chromosome lengths for BSgenome.Rnorvegicus.UCSC.rn5...
> Calculating genomic coordinates...Error in vector(length = supersi
>
> ze_chr[length(chromosomes)], mode = "character") :
>   vector size cannot be NA/NaN
>
>
> Thank you very much!
>
> thanks,
> Yuting
>
>  -- output of sessionInfo():
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] BSgenome.Rnorvegicus.UCSC.rn5_1.3.17 BiocInstaller_1.10.3
> [3] MEDIPS_1.10.0                        DNAcopy_1.34.0
> [5] BSgenome_1.28.0                      Biostrings_2.28.0
> [7] GenomicRanges_1.12.5                 IRanges_1.18.3
> [9] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.95-4.1   Rsamtools_1.12.4 XML_3.98-1.1     biomaRt_2.16.0
> [5] bitops_1.0-6     gtools_3.0.0     stats4_3.0.1     tools_3.0.1
> [9] zlibbioc_1.6.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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