GeneGA-class: Class "GeneGA"

In GeneGA: Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm

Description

GeneGA class for representing the GeneGA results

Slots

All the slots of the GeneFoldGA class, plus the following slots:

CAI_value:

Object of class "numeric". If ramp and specified region are not intersecting, it denotes the CAI values of all final population, otherwise, it denotes the CAI values of the intersected region of all final population.

CAI_value_:

Object of class "numeric". When ramp and specified region are intersecting, it denotes the CAI values of the specified region that not intersecting with the specified region of all final population.

free_en_set:

Object of class "numeric". The mean of minimum free energy of the population.

CAI_value_set:

Object of class "numeric". If ramp and specified region are not intersecting, it denotes the mean of CAI values of the population, otherwise, it denotes the mean CAI values of the the intersected region of the population.

CAI_value_set_:

Object of class "numeric". When ramp and specified region are intersecting, it denotes the mean CAI values of the specified region that not intersecting with the specified region of the population.

free_en_set02:

Object of class "numeric". The maximum of minimum free energy of the population.

CAI_value_set02:

Object of class "numeric". If ramp and specified region are not intersecting, it denotes the maximum of CAI values of the population, otherwise, it denotes the maximum CAI values of the the intersected region of the population.

CAI_value_set02_:

Object of class "numeric". When ramp and specified region are intersecting, it denotes the maximum CAI values of the specified region that not intersecting with the specified region of the population.

Methods

show

signature(object = "GeneGA"): Displaying the results of GeneGA and GeneFoldGA, the first three distinctive and optimum sequences can be returned, as well as their overall evaluation values, CAI values and minimum free energys.

plotGeneGA

signature(object = "GeneGA"): Visualizing the variation of optimized and mean overall evaluation values and variable values during the progress that genetic algorithm performed. Furthermore, the plot also can be used to check the results whether well converged.

See Also

GeneGA, GeneFoldGA, GeneCodon, show-methods, plotGeneGA-methods

GeneGA documentation built on Nov. 8, 2020, 8:17 p.m.