Thanks Steve, I already did it and it went perfectly well.
I was just trying to understand the functions David wrote, so that I can use them maybe for other queries. Unfortunately I wasn't able to add a condition for the fact that there is a third parameter to be compared. I would still ove to know whether there is a way of adding such a perameter. I tried to do it with a third argument in this line: any( apply(locs, 1, function(x){vec["start"]>x[2] & vec["start"]<=x[3] & * as.character(vec["chr"])==as.character(x["chr"]*) but it doesn't seems to work at all. Thanks for the help anyway Assa On Wed, Oct 26, 2011 at 15:33, Steve Lianoglou < mailinglist.honey...@gmail.com> wrote: > Hi, > > On Wed, Oct 26, 2011 at 8:17 AM, Assa Yeroslaviz <fry...@gmail.com> wrote: > > Hi David, > > > > your function works just fine if I take nly the region into account. But > > unfortunately it does not consider the first column of the chromosomes. > > There can be an overlap between the two tables only if the regions are on > > the same chromosome. This is why the first column of both tables is a > > prerequisite for the analysis. > > > > I treid somehow to create a second argument to consider this, but until > now > > without success. > > Well, bioconductor has packages to deal with this type of data, and > these type of queries (overlaps) very efficiently. > > Martin Morgan had sent you an email earlier explaining how you can use > the GenomicRanges packages to get what you're after ... I (highly) > suggest you go that route. > > HTH, > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.