Index

NAME
SYNOPSIS
DESCRIPTION
METHODS
EXAMPLES
SEE ALSO
COPYRIGHT
AUTHORS

NAME

InSilicoSpectro::InSilico::RetentionTimer::Petritis Prediction of peptide retention time by neural network training

SYNOPSIS

  # creates a retention time predictor
  my $rt = InSilicoSpectro::InSilico::RetentionTimer::Petritis->new;

  # trains the predictor
  $rt->learn( data=>{expseqs=>['ELGFQG','HPGDFGADAQAAMSK','LSSPATLNSR','RFIK'],
              exptimes=>[1314,1194,1152,1500]},mode=>'verbose',
	      maxepoch=>100, sqrerror=>1e-3,mode=>'verbose',
	      nnet=>{learningrate=>0.05},layers=>[{nodes=>20},{nodes=>2},{nodes=>1}] );

  # predicts retention time for a peptide
  $rt->predict( peptide=>'ACFGDMKWVTFISLLRPLLFSSAYSRGVFRRDTHKSEIAHRFKDLGE' );

  # saves the network
  $rt->write_xml(confile=>'nnet01.xml');

  # retrieves a previously saved network
  $rt->read_xml(confile=>'nnet00.xml');

  # assigns a calibrator to the predictor
  $ec=InSilicoSpectro::InSilico::ExpCalibrator->new( fitting=>'spline' );

  # fits the calibrator from expermiental values
  $rt->calibrate( data=>{calseqs=>['ELGFQG','HPGDFGADAQAAMSK','LSSPATLNSR','RFIK'],
                 caltimes=>[1314,1194,1152,1500]},calibrator=>$ec );

  # save current calibrator
  $rt->write_cal( calfile=>$file );

  # retrieve previously saved calibrator
  $rt->read_cal ( calfile=>$file );

DESCRIPTION

Predicts HPLC retention time for peptides

METHODS

my $rt=InSilicoSpectro::InSilico::RetentionTimer::Petritis->new(%h )

%h contains a hash

$rt->learn( data=>{expseqs=>\@seqs,exptimes=>\@times}, mode=>'verbose',maxepoch=>100, sqrerror=>1e-3,mode=>'verbose', nnet=>{learningrate=>0.05},layers=>[{nodes=>20},{nodes=>2},{nodes=>1}] ); );

Trains the network from experimental data given in the arrays (@seqs,@times).

maxepoch, sqrerror : train the network until sse < sqrerror or maxepoch
nnet=>{%h} : hash with options for method AI::NNFlex::Backprop->new( %h )
layers=>[{%h1},{%h2},{%h3}] : hashes with options for the 3 layers as defined by method AI::NNFlex::Backprop->add_layer( %hi )
mode=>'silent'|'verbose': Method used for fitting

$rt->predict(peptide=>$str)

Predicts retention time for the peptide

$rt->predictor(peptide=>$str)

Same as predict() but without experimental fitting

$rt->calibrate( data=>{calseqs=>\@str,caltimes=>\@val},fitting=>$str );

Trains the predictor with experimental data and the chosen fitting method

fitting=>'linear'|'spline': Method used for fitting

$rc->filter( filter=>$pc,error=>$str )

Filter experimental data in $rc->{data} by a cutting threshold of relative prediction error of $pc (in %).

error=>'relative'|'absolute': Type of error for filtering.

$rt->writexml( confile=>$file )

Saves network into a file

$rt->readxml( confile=>$file )

Retrieves a previously saved network

$rt->write_cal( calfile=>$file );

Save current calibrator.

$rt->read_cal ( calfile=>$file );

Retrieve a previously saved calibrator.

$rt->set($name, $val)

Set an instance paramter.

$rt->get($name)

Get an instance parameter.

EXAMPLES

see InSilicoSpectro/t/InSilico/testPetritis.pl script

COPYRIGHT

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

AUTHORS

Pablo Carbonell, Alexandre Masselot, www.genebio.com

InSilicoSpectro::InSilico::RetentionTimer::Petritis - InSilicoSpectro::InSilico::RetentionTimer::Petritis documentation