Martin, Again, thanks for your time to educate. All is clear. The problem was mine. --Malcolm On 9/1/12 8:49 AM, "Martin Morgan" <mtmorgan at="" fhcrc.org=""> wrote: >On 08/31/2012 04:22 PM, Cook, Malcolm wrote: >> Herve et al, >> >> I believe that transcriptLocs2refLocs is implemented incorrectly for >> negative strands. >> >> The bug appears in the example of its use you provided in >> https://stat.ethz.ch/pipermail/bioconductor/2011-March/038173.html >> >> I think you will agree that the third result should be: >> [[3]] >> [1] 5899 6291 > >Hi Malcolm > >In the example the exon coordinates (always in 1-based 'leftmost' >cooredinates') are > >start: c(6291L, 5278L) > end: c(6500L, 5899L) > >so on the minus strand the 5' -> 3' transcript is from 6500 --> 6291 and >then 5899 -> 5271, and is 832 nt long. > >The first (5') nucleotide on the transcript comes from position 6500, >the 832nd nucleotide comes from the 3' ('leftmost', when the exon is on >the minus strand) end of the second exon, at genomic coordinate 5278. >These are the values that transcriptLocs2refLocs returns. > >Martin > >> >> As a workaround, I have implemented a version in R using a new generic, >> named `at` >> >> >> >> >> I would be happy to receive confirmation that this is a bug, and >>comments >> from anyone on the approach to the workaround I have adopted, especially >> as regards performance comparison with >> >> Thanks, >> >> Malcolm Cook >> Stowers Institute for Medical Research >> >> _______________________________________________ >> 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 >> > > >-- >Computational Biology / Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. >PO Box 19024 Seattle, WA 98109 > >Location: Arnold Building M1 B861 >Phone: (206) 667-2793