I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and challenging statistical problems in current molecular biology and I am hoping that making these procedures available to the R community will encourage people to get involved. Some links to useful sites for learning about molecular biology can be found at www.luc.ac.be/~jlindsey/url.html Comments and suggestions for further inclusions in the library are very welcome. Jim -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Jim, Thanks for making this library available. As a trained human geneticist, but a pharmaceutical scientist who spends most of my time working on non-genetics projects using S-Plus/RWin/R (Linux), I've often thought that it would be nice to stick with the same set of tools when I put my geneticist/bioinformaticist hat back on. In fact, I will often reformat various genetics/DNA data sets for analysis in R. Having said that, I would be happy to contribute to further development of the library. I will look for opportunities to use it and pass bug-reports along to you. I will also consider ways that it could be enhanced. If there are other ways that you feel I could contribute, please let me know. I have five years of experience programming at various levels in S/R, and am comfortable coding in C/C++. Regards, Matt Matthew R. Nelson, Ph.D. Information Scientist Esperion Therapeutics, Inc. 3621 S. State St. 695 KMS Place Ann Arbor, MI 48108 Phone: (734) 332-0506 x235 Fax: (734) 332-0516 email: mnelson at esperion.com web: http://www.esperion.com -----Original Message----- From: Jim Lindsey [mailto:jlindsey at alpha.luc.ac.be] Sent: Thursday, March 23, 2000 12:44 PM To: r-announce at stat.math.ethz.ch Subject: dna library I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and challenging statistical problems in current molecular biology and I am hoping that making these procedures available to the R community will encourage people to get involved. Some links to useful sites for learning about molecular biology can be found at www.luc.ac.be/~jlindsey/url.html Comments and suggestions for further inclusions in the library are very welcome. Jim -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. -.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._. _._ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
This looks very promising. I'll show it to our StatGen people.
Three points.
1. In interface.c at line 101 you have
char seqname[]
which gcc doesn't like (it wants a length for the array). It doesn't
seem
to be used anywhere so I commented it out.
2. In interface.c at line 152 you have
init_matrix()
when I think you mean
init_matrix(error)
3. The documentation for flip has \code{@}, which doesn't get processed
correctly. I changed it to \@.
-thomas
Thomas Lumley
Assistant Professor, Biostatistics
University of Washington, Seattle
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Sorry, that last message should have gone to Jim, not to the list. I deleted the wrong header line. -thomas -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Hi Jim, Thank you very much!!!. I am very happy with my job in the University. Finally, I am using properly my statistical skills. I have a question ? Where I can load dowon a C compiler for MS Windows system? Best regards, Pablo. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._