Thanks for the update. -steve On Wed, Dec 29, 2010 at 6:50 PM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > Thanks Steve. Yes, the docs had it backwards. It was already fixed in devel; > I just pushed it back to release. Sorry that this consumed your time. > > Michael > > On Tue, Dec 28, 2010 at 9:28 AM, Steve Lianoglou > <mailinglist.honeypot at="" gmail.com=""> wrote: >> >> Hi, >> >> I think the holiday-over-eating is affecting my reading comprehension >> skills. I'm having problems groking the documentation/functionality of >> (for instance) precede, as it seems to return an integer vector that's >> "backwards to" the documentation. >> >> For instance, for `precede(x, subject)`, the docs say: >> >> ?precede returns an integer vector of the index of range in subject >> ?that ends before and closest to the start of each range in x. Note >> ?that any overlapping ranges are excluded. NA is returned when there >> ?are no qualifying ranges in subject. >> >> I am expecting an integer vector that is as long as x that indexes >> *into* the subject ranges. I'm getting that, but I also expect that >> the i'th value of the returned integer vector should be the index into >> `subject` that is closest to and precedes the i'th range in x. >> >> Using the second example from the docs, we don't get this at all ... >> in fact we get something of the opposite: >> >> ?query <- IRanges(c(1, 3, 9), c(3, 7, 10)) >> ?subject <- IRanges(c(3, 2, 10), c(3, 13, 12)) >> >> ?p <- precede(query, subject) # c(3L, 3L, NA) >> >> The way I'm reading the docs, shouldn't p[1] indicate that >> subject[p[1]] "ends before and [is] closest to" query[1]? The returned >> vector is rather telling me that query[1] precedes subject[p[1]]. >> >> So, shouldn't the docs read something more like "precede returns an >> integer vector of the index into the range of `subject` that >> immediately follows the corresponding range in x (the query) ... >> overlaps ignored, etc." Or something similar, no? >> >> R> sessionInfo() >> R version 2.12.1 (2010-12-16) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] IRanges_1.8.7 >> >> loaded via a namespace (and not attached): >> [1] tools_2.12.1 >> >> Thanks, >> -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 >> >> _______________________________________________ >> 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 > > -- 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