Chromosome: The representation of a set of genes for genetic algorithms

In galgo: Genetic Algorithms for Multivariate Statistical Models from Large-Scale Functional Genomics Data

Description

Represents a set of genes for the genetic algorithm. The chromosome contains all current values of each gene and will be evaluated using a “fitness” function similar to those defined by Goldberg. The fitness function normally depends on the Galgo object.

See references for Genetic Algorithms.

Usage

Chromosome(id=0,
	genes=list(),
	getValues=function(x, ...) unlist(lapply(x, ...)),
	decode=function(x) genes(x),
	values=list(),
	...)

Arguments

id	A way to identify the object.
genes	A list of defined Gene objects composing the chromosome.
getValues	A function to be evaluated for every gene to obtain a value. In general, the result could be any object in a list. In particular, the default is a vector of current gene values.
decode	A function that converts the chromosome representation in real values. It is used mainly for output purposes and for frequency counting. It has no effect for variable selection in microarray data since the default decode is directly the gene value.
values	The specific initial values. If value is not specified, getValues function is ran to obtain initial values.
...	Other user named values to include in the object.

Class

Package: galgo
Class Chromosome

Object
~~|
~~+--Chromosome

Directly known subclasses:

public static class Chromosome
extends Object

Fields and Methods

Methods:

	as.double	Converts the chromosome values (genes) to its numerical representation.
	clone	Clones itself and its genes.
	decode	Converts the gene values to user-readable values.
	generateRandom	Generates random values for all genes in the chromosome.
	genes	Converts the genes values to a numeric vector.
	length	Gets the number of genes defined in the chromosome.
	mutate	Mutates a chromosome in specific positions.
	newCollection	Generates a list of chromosomes cloning the original chromosome object.
	newRandomCollection	Creates a list of cloned chromosomes object with its internal values generated by random.
	print	Prints the representation of the chromosome object.
	reInit	Erases all internal values in order to re-use the object.
	summary	Prints the representation of the chromosome object and all its genes.

Methods inherited from Object:
as.list, unObject, $, $<-, [[, [[<-, as.character, attach, clone, detach, equals, extend, finalize, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save

Author(s)

Victor Trevino. Francesco Falciani Group. University of Birmingham, U.K. http://www.bip.bham.ac.uk/bioinf

References

Goldberg, David E. 1989 Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley Pub. Co. ISBN: 0201157675

See Also

Gene. Niche. World. Galgo. BigBang.

Examples

  cr <- Chromosome(genes=newCollection(Gene(shape1=1, shape2=100),5))
  cr

galgo documentation built on May 2, 2019, 4:20 a.m.