[BioC] ChIPpeakAnno, building annotations

[Hans-Rudolf Hotz]

Marc

Use "rtracklayer" which interfaces with the UCSC genome browser. You 
have access to all the tables with the "track" function. Have a look at 
help for "track".   -  This corresponds to using the following web page:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start

In your case, you need the "RepeatMasker" track. From the data you get 
back, you need to select for the different alu types. You do get all 
repeats.

For CpG islands, take the "CpG Islands" track


Hans



On 08/24/2010 04:52 PM, Marc Noguera wrote:
> Hi all,
> I have been learning to use ChIPpeakAnno package to annotate the peaks I
> obtain with CHiPseq experimetns. I see that, useing biomaRt, i can get
> to some annotation on ensembl and annotate the peaks according to TSS,
> exon, miRNA and some other features.
> I would like, also, to be able to search for repetitive elements, such
> as ALUs and CpG Islands. Is that kind of information also accessible
> using biomaRt? I can't seem to find it. If not how should I proceed?
>
> Thanks in advance
>
> Marc
>