Hello, I am new to using the Genomic Ranges package and manipulating GRanges objects but I am currently attempting to overlap two GRanges objects. This is the command I used - findOverlaps(duke.dnase, h1.midmethgr, maxgap = 0L, minoverlap = 1L,type = "any", select ="all") where - duke.dnase and h1.midmethgr are the two GRanges objects. I am wondering how to play with the parameters in order to perform a more stringent overlap - I would like to modify with the number of base pairs that need to overlap between coordinates in order for it to be considered a hit. I am unsure as to what mioverlap = 1L means for this purpose. I would really appreciate your help. Thank you, Kurinji Graduate Student Johns Hopkins University/University of Southern California [[alternative HTML version deleted]]

minoverlap is the number of bases in the query range that must overlap with the subject range in order for it to be considered an overlap. for example foo = GRanges( c('chr1','chr1','chr1'), IRanges( start=c(1, 5, 10), end=c(10,10,10) ), strand='*') bar = GRanges( c('chr1'), IRanges( start=1, end=10 ), strand='*' ) show(foo) show(bar) findOverlaps(foo, bar, minoverlap=5) or perhaps more illustratively, subsetByOverlaps(foo, bar, minoverlap=1) subsetByOverlaps(foo, bar, minoverlap=5) subsetByOverlaps(foo, bar, minoverlap=10) Does this make sense? I didn't cover gapping, but Herve can answer that 1000x better than I can. On Tue, Jun 5, 2012 at 1:11 PM, Kurinji Pandiyan <kurinji.pandiyan@gmail.com> wrote: > Hello, > > I am new to using the Genomic Ranges package and manipulating GRanges > objects but I am currently attempting to overlap two GRanges objects. This > is the command I used - > > findOverlaps(duke.dnase, h1.midmethgr, maxgap = 0L, minoverlap = 1L,type = > "any", select ="all") > > where - duke.dnase and h1.midmethgr are the two GRanges objects. > > I am wondering how to play with the parameters in order to perform a more > stringent overlap - I would like to modify with the number of base pairs > that need to overlap between coordinates in order for it to be considered a > hit. I am unsure as to what mioverlap = 1L means for this purpose. > > I would really appreciate your help. > > Thank you, > Kurinji > > Graduate Student > Johns Hopkins University/University of Southern California > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]