[BioC] MEDIPS.createSet error

Vining, Kelly Kelly.Vining at oregonstate.edu
Fri Mar 28 18:42:33 CET 2014

I'm coming back to a MEDIPS project after a long pause, and am having trouble reading in my .bam files. I'm using a custom reference genome that Lukas Chavez kindly helped me to make into a BSgenome object.  I'm not sure how to address the error message below. I hope it doesn't mean there is something wrong with my reference genome...

> budFall1_MEDIP = MEDIPS.createSet(file="FallBud_brep1_aln_sorted.bam", BSgenome=BSgenome, extend=300, uniq=TRUE, shift=0, window_size=1000)
Reading bam alignment FallBud_brep1_aln_sorted.bam
Total number of imported short reads: 21038273
Extending reads...
Creating GRange Object...
Extract unique regions...
Number of unique short reads: 17855868
Calculating genomic coordinates...Error in vector(length = supersize_chr[length(chromosomes)], mode = "character") :
  vector size cannot be NA/NaN

Thanks for help,
Kelly V.

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