[BioC] How to get the all CpG sites genome postion for mm9?

[Aaron Statham]

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>
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-- 
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