Hi Aaron, It is helps. Thanks. On Fri, Jan 14, 2011 at 2:06 AM, Aaron Statham <a.statham at="" garvan.org.au=""> wrote: > On 14 January 2011 08:04, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: >> I have little question. How can I get the all CpG sites genome postion >> for mm9? It is the positions for all CpG sites for mm9. >> >> Thanks. > > Here's a quick example for hg18 off the top of my head > > > library(BSgenome.Hsapiens.UCSC.hg18) > chrs <- names(Hsapiens)[!grepl("upstream", names(Hsapiens))] #filter > out the "upstream" chromosomes > CGs <- lapply(chrs, function(x) start(matchPattern("CG", Hsapiens[[x]]))) > names(CGs) <- chrs > > Now CGs is a list of integer positions of CpG residues in hg18 ie > >> str(CGs) > List of 49 > ?$ chr1 ? ? ? ? : int [1:2281713] 469 471 484 489 493 497 525 542 563 571 ... > ?$ chr2 ? ? ? ? : int [1:2156723] 1 215 270 296 360 379 385 391 398 405 ... > ?$ chr3 ? ? ? ? : int [1:1622113] 35156 35321 35688 35759 35767 35850 > 36519 36591 37603 37817 ... > > and so on > > Cheers, > Aaron> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Aaron Statham > Postgraduate Scholar, Cancer Epigenetics > Garvan Institute of Medical Research?? Tel: (02) 9295 8393 > 384 Victoria St Darlinghurst 2010?? Fax: (02) 9295 8316 > NSW Australia? ? ? ?? email: a.statham at garvan.org.au > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >