[BioC] find overlap of bed files of different length

[Duke]

Hi all,

I need to find overlap between a text file (BED format) and a gene 
reference. The BED file contains sequence of different lengths, and I 
need to find all the sequences that lye inside the gene (meaning 
overlapping percentage is 100%). I found findOverlaps function in 
GenomicRanges, but the parameter to control overlap (minoverlap) does 
not let me control percentage.

Anybody has any suggestion for me?

Thanks so much,

D.