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.IX Title "Bio::Tools::PSort::SVMLoc 3pm"
.TH Bio::Tools::PSort::SVMLoc 3pm "2018-10-22" "perl v5.24.1" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::Tools::PSort::SVMLoc \- Perl bindings for the libsvm Support Vector Machine library in Psortb.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::PSort::SVMLoc;
\&
\&  # Load the model stored in the file \*(Aqsample.model\*(Aq and Frequent Patterns in \*(AqFreqPatt\*(Aq
\&  $svm = new Bio::Tools::PSort::SVMLoc(Model => \*(Aqsample.model\*(Aq, FreqPattern => \*(AqFreqPatt\*(Aq);
\&
\&  # Classify a sequence in $seq, do not include FASTA headers!
\&  $svm\->classify($seq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::Tools::PSort::SVMLoc implements a Support Vector Machine for Perl.  Support Vector
Machines provide a method for creating classifcation functions from a set of
labeled training data, from which predictions can be made for subsequent data
sets.
.PP
Bio::Tools::PSort::SVMLoc is a stripped down version of Algorithm::SVM design specifically
for PSortb.  If you need functionality such as training of \s-1SVM,\s0 please use that module
instead.
.SH "CONSTRUCTOR"
.IX Header "CONSTRUCTOR"
.Vb 2
\&  # Load an existing SVM.
\&  $svm = new Bio::Tools::PSort::SVMLoc(Model  => \*(Aqsample.model\*(Aq, FreqPattern => \*(AqFreqPatt\*(Aq);
.Ve
.PP
A Bio::Tools::PSort::SVMLoc object must be created loaded from an existing
model file.
.PP
An existing \s-1SVM\s0 is loaded from a file using the Model named parameter and the
frequent patterns set.
The model file should be of the format produced by the svm\->train program
(distributed with the libsvm library) or from the \f(CW$svm\fR\->\fIsave()\fR method in
Algorithm::SVM.
.SH "METHODS"
.IX Header "METHODS"
.Vb 1
\&  $result = $svm\->classify($seq);
.Ve
.PP
The classify method is used to classify a set of data according to the
loaded model.  The method accepts a single parameter, which should be
a protein sequence object.  Returns a floating point number
corresponding to the predicted value.
.SH "MAINTAINER"
.IX Header "MAINTAINER"
Matthew Laird <matt@brinkman.mbb.sfu.ca>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
The libsvm homepage:
http://www.csie.ntu.edu.tw/~cjlin/libsvm/
.SH "ACKNOWLEDGEMENTS"
.IX Header "ACKNOWLEDGEMENTS"
Thanks go out to Fiona Brinkman and the other members of the Simon Fraser
University Brinkman Laboratory for providing me the opportunity to develop
this module.  Additional thanks go to Chih-Jen Lin, one of the libsvm authors,
for being particularly helpful during the development process.