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PTModel

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Trains a model for the prediction of proteotypic peptides from a training set.

Web Documentation for PTModel

Options

version
Version of the tool that generated this parameters file.
c
the penalty parameter of the svm
svm_type
the type of the svm (NU_SVC or C_SVC)
nu
the nu parameter [0..1] of the svm (for nu-SVR)
kernel_type
the kernel type of the svm
degree
the degree parameter of the kernel function of the svm (POLY kernel)
border_length
length of the POBK
k_mer_length
k_mer length of the POBK
sigma
sigma of the POBK
max_positive_count
quantity of positive samples for training (randomly chosen if smaller than available quantity)
max_negative_count
quantity of positive samples for training (randomly chosen if smaller than available quantity)
redundant
if the input sets are redundant and the redundant peptides should occur more than once in the training set, this flag has to be set
additive_cv
if the step sizes should be interpreted additively (otherwise the actual value is multiplied with the step size to get the new value
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
skip_cv
Has to be set if the cv should be skipped and the model should just be trained with the specified parameters.
number_of_runs
number of runs for the CV
number_of_partitions
number of CV partitions
degree_start
starting point of degree
degree_step_size
step size point of degree
degree_stop
stopping point of degree
c_start
starting point of c
c_step_size
step size of c
c_stop
stopping point of c
nu_start
starting point of nu
nu_step_size
step size of nu
nu_stop
stopping point of nu
sigma_start
starting point of sigma
sigma_step_size
step size of sigma
sigma_stop
stopping point of sigma

Input Ports

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input file with positive examples [idXML]
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input file with negative examples [idXML]

Output Ports

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output file: the model in libsvm format [txt]
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output file with additional model parameters when using the OLIGO kernel [paramXML]
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output file with the used training dataset when using the OLIGO kernel [txt]

Views

PTModel Std Output
The text sent to standard out during the execution of PTModel.
PTModel Error Output
The text sent to standard error during the execution of PTModel. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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