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

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.)

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