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

[Fabrice Tourre]

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>
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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
>
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