[BioC] error with MEDIPS.CpGenrich when using extend

Elisabetta Manduchi manduchi at pcbi.upenn.edu
Thu Oct 20 22:36:24 CEST 2011


Hello,
I'm using MEDIPS version 1.20.0 on R version 2.13.2 with a Sus scrofa 2 
BSgenome package that I've built according to instructions.

I can run the MEDIPS.CpGenrich function in default mode (i.e. without 
setting a value for extend)  on my set. But, if I try to provide a value 
for the extend parameter I get the below warning and NA ni the outputs.

Could you advice?
Thanks,
Elisabetta

----
> er.aa=MEDIPS.CpGenrich(data=aa.set,extend=400)
Preprocessing...
   |                                                                      | 
0%
Calculating CpG density for given regions...
   |======================================================================| 
100%
Calculating CpG density for the reference genome... 
BSgenome.Sscrofa.UCSC.susScr2
Warning message:
In sum(width(y)) : Integer overflow - use sum(as.numeric(.))
> er.aa
$regions.CG
[1] 348336822

$regions.C
[1] 5673567676

$regions.G
[1] 5682126095

$regions.relH
[1] NA

$regions.GoGe
[1] NA

$genome.C
[1] 465046343

$genome.G
[1] 464928778

$genome.CG
[1] 26913896

$genome.relH
[1] 1.206199

$genome.GoGe
[1] 0.2777484

$enrichment.score.relH
[1] NA

$enrichment.score.GoGe
[1] NA



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