[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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