Thanks Valerie. Yue On 2012-04-26, at 2:58 PM, Valerie Obenchain wrote: > Hi Yue, > > Yes, the vignette was incorrect. It has been fixed in version 1.8.4 in release and 1.9.9 in the devel branch. These versions should be available in ~24 hours through biocLite() or now from the svn repositories. Thanks for pointing out this bug and sorry we missed the previous discussion of the topic. > > We would suggest using > > not.exons <- aligns[!aligns %in% exonRanges] > > as posted in the last thread. > > Valerie > > > > > > The vignette has been updated in release devel 1.9.9 > > > On 04/24/2012 06:52 PM, Yue Li wrote: >> Dear List, >> >> This is a question that has been asked before in the message titled "GenomicRanges Use Cases - subsetByOverlaps". But I just want to confirm that there is a mistake in section 3.4 of the vignette GenomicRangesUseCases.pdf. >> >> Basically, it was claimed in the section to look for "ranges that did not overlap with any of the known exons from Saccharomycess cerevisiae." using: >> >> filtData<- subsetByOverlaps(aligns, exonRanges) >> >> However, filtData in fact contains exactly the read regions that DO overlap with the known exons. >> >> To get ""ranges that did not overlap with any of the known exons", it's been suggested in that thread to instead use: >> >> not.exons<- aligns[!aligns %in% exonRanges] >> >> Is the latter in fact the CORRECT way to do it or the way in the vignette? >> >> Thanks in advance! >> Yue >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >