[BioC] find overlap of bed files of different length

[Duke]

On 1/29/11 9:08 PM, Christoph Bartenhagen wrote:
> Hi,
>
> although this is a bioconductor mailing list, I'd suggest to take a 
> look at an independent, non-R program in this case: BEDTools.
> It has several functions to process BED-files including a method to 
> find overlaps between two BED-files (I think it's called intersectBED 
> and you might need to convert your gene reference file into 
> BED-format; columns for chromosome, start and end are sufficient). 
> Here you can also specifiy the mean overlapping percentage. BEDTools 
> is not very difficult to get into and has a quite good manual in my 
> opinion.
> Sorry I don't know a suitable solution in R, but this should do 
> exactly what you want.
>

Thanks for your suggestion Christoph. I will try BEDTools if I can not 
get it to work with R.

D.