[BioC] MEDIPS saturation error

[Yuting Liu [guest]]

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


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