Hi Andreia,

You might want to have a look at the GenomicFeatures package and the
GenomicRanges Package.  If you read the corresponding vignettes, you
should find examples that I think do a lot of what you are talking about
here.

http://www.bioconductor.org/packages/devel/bioc/html/GenomicFeatures.html

http://www.bioconductor.org/packages/devel/bioc/html/GenomicRanges.html


  Marc




On 05/14/2010 05:43 AM, Andreia Fonseca wrote:
> Dear List,
>
> I have a file with the hits of my sequences of small RNA (18-30bp) in the
> human genome and I have downloaded the all the annotation of the human
> genome from UCSC. What I want is to annotate my sequences by finding
> ovelaping between the positions of my sequences the the information
> available from the tables I have downloaded from UCSC. So in the file which
> maps my sequences (produced using microRazers) in the human genome I have
> the folowing structure:
>
> sequence sequence length strand chromosome start end score alignment length
>
> I don't want to do this with biomart, because it will be too slow making all
> the queries. However I have found the package IRanges, which has the overlap
> function, but I am not understanding how the two tables - the query and the
> target tables - should be stored and how to make the overlapping. Can
> someone give me a hint?
> With kind regards,
> Andreia
>
>   
>
>
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