Hi, On Sat, Feb 6, 2010 at 11:40 AM, Martin Morgan <[email protected]> wrote: > On 02/06/2010 07:29 AM, Steve Lianoglou wrote: >> Hi, >> >> On Sat, Feb 6, 2010 at 4:17 AM, Steve Lianoglou >> <[email protected]> wrote: <snip>
>> R> r$strand >> [1] + + >> Levels: + - * > > I notice that your levels are different from mine; what does > levels(strand()) say? what's your locale? (sesssionInfo() ;) -- > Rsamtools and strand() in general was trying to be locale-independent, > but this seems not to be the case... > > The workaround is likely to work in a "C" locale, ?Sys.setlocale Sorry, I pasted the sessionInfo() in the first post and neglected to do so in the second, but the locale is: locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 Also: > ok, I think it's this > > ------------------------------------------------------------------------ > r44085 | p.aboyoun | 2010-01-19 15:16:56 -0800 (Tue, 19 Jan 2010) | 2 lines > Changed paths: > M /trunk/madman/Rpacks/BSgenome/R/strand.R > > Added support for Rle strand column in strand,DataTable method. > Also made "+" the first level of strand factor. > ------------------------------------------------------------------------ > > which changed the order of strand levels. This will take a bit of > coordination on our part. Thanks for the reports. So, being that you're more familiar with these codebases than I could hope to be, do you think the problem lies strictly in the BSgenome package? Or should I look at Rsamtools code, too? Do you reckon running with a checkout of the version of the BSgenome repo at the revision before r44085 will be OK to sidestep the issue, or should I backtrack my Rsamtools, too? I will, of course, try a few different permutations to see what works, in the meanwhile, so I'm not expecting you to take time to try that yourself. If you had some intuition, though, I'd appreciate your point of view :-) 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
