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

Dear Elisabetta, it seems that sum() doesn't automatically coerce so in this case we had to adapt the MEDIPS.CPGenrich (MEDIPS 1.3.3) function which should be available within the next days in the dev. In the meanwhile you could try to change sum(width(y)) as sum(as.numeric(width(y))) in your local version ".../MEDIPS/R/MEDIPS.CPGenrich.R". If you have any further problems don't hesitate to contact us. Best wishes, Joern