Ying, I modified BED2RangedData and GFF2RangedData per your suggestions. The Version is devel 2.5.1 with revision 64831. Thanks again for your great suggestions! Best regards, Julie On 4/3/12 9:34 AM, "Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: > Ying, > > Thanks so much for willing to share the code! We would be happy to > incorporate your code in makeVenndiagram. > > Sorry that I missed your earlier email regarding strand conversion. The > reason I convert it to 1/-1 is to be compatible with other functions. It is > for the best to convert it to +/- in all functions. We will do. > > Thanks again for your constructive suggestions and willing to share your > code! > > Best regards, > > Julie > > > On 4/2/12 6:16 PM, "Ying Wu" <daiyingw at="" usc.edu=""> wrote: > >> Hi Dr Zhu, >> I am writing to you again to ask you about the reasons why you convert >> strand +/- to 1/-1 in this BED2RangedData(). I was hoping you could >> instead keep it as +/-/* because you cannot change RangedData objects >> generated by this function into GRanges object unless the strand is >> +/-/*. The code in question can be found on line 38-39 in >> BED2RangedData.R example code follows: >> g1 = read.table("my.bed", sep="\t") >> g1.r = BED2RangedData(g1) >> g1.g = as(g1.r, "GRanges") >> >> I use GRanges object instead of RData since I find it easier to have >> things not arranged by space (though less efficient). On the topic of >> efficiency, I was wondering if you've looked into Michael Lawrence's >> method here: >> https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2010-March/001035.html >> I do not subscribe to this list but I found this thread while looking >> for a way to speed up the findOverlappingPeaks comparison in >> makeVennDIagram. I have implemented this method for a 3-way venn diagram >> and it is quite a bit faster than makeVennDiagram(). Digging into your >> code on bioconductor, I believe the time bottleneck is in lapply >> statement of findOverlappingPeaks (I am probably wrong about this since >> I did not test things thoroughly). However, if you are interested, I >> could send you the code I wrote to implement what Michael mentioned in >> that thread. >> >> Best, >> Ying Wu >