[R] stringdot ?

From: <renata.camargo05_at_ntlworld.com>
Date: Tue, 29 Jul 2008 12:38:44 +0100


Dear all,

I am using kernlab package in R, and I have amino acid sequences with different lenghts as input for a SVM and I need to go through this sequences using windows (sliding or fixed) of size X. Does anyone has any suggestions about which function I should use? I thought I could use stringdot, but I am not sure whether it will do what I need.., I have defined my stringdot as:

mystringdot <- stringdot(length = 7, lambda = 0.5, type = "sequence", normalized = TRUE)

and my svm as:

ksvm(mydata[,1],data=mydata,type="C-svc",kernel=mystringdot,C=10)

but it doesn't work.

Thank you ever so much, Renata



Email sent from www.virginmedia.com/email Virus-checked using McAfee(R) Software and scanned for spam

R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Tue 29 Jul 2008 - 11:41:08 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Tue 29 Jul 2008 - 12:32:51 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive