dGAselID {dGAselID}

dGAselID

Description

Initializes and starts the search with the genetic algorithm.

Usage

dGAselID(x, response, method = knn.cvI(k = 3, l = 2), trainTest = "LOG",
  startGenes, populationSize, iterations, noChr = 22, elitism = NA,
  ID = "ID1", pMutationChance = 0, nSMutationChance = 0,
  fSMutationChance = 0, lSDeletionChance = 0, wChrDeletionChance = 0,
  transposonChance = 0, randomAssortment = TRUE, embryonicSelection = NA,
  EveryGeneInInitialPopulation = TRUE, nnetSize = NA, nnetDecay = NA,
  rdaAlpha = NA, rdaDelta = NA, ...)

Arguments

x

Dataset in ExpressionSet format.

response

Response variable

method

Supervised classifier for fitness evaluation. Most of the supervised classifiers in MLInterfaces are acceptable. The default is knn.cvI(k=3, l=2).

trainTest

Cross-validation method. The default is "LOG".

startGenes

Genes in the genotypes at initialization.

populationSize

Number of genotypes in initial population.

iterations

Number of iterations.

noChr

Number of chromosomes. The default value is 22.

elitism

Elite population in percentages.

ID

Dominance. The default value is "ID1". Use "ID2" for Incomplete Dominance.

pMutationChance

Chance for a Point Mutation to occur. The default value is 0.

nSMutationChance

Chance for a Non-sense Mutation to occur. The default value is 0.

fSMutationChance

Chance for a Frameshift Mutation to occur. The default value is 0.

lSDeletionChance

Chance for a Large Segment Deletion to occur. The default value is 0.

wChrDeletionChance

Chance for a Whole Chromosome Deletion to occur. The default value is 0.

transposonChance

Chance for a Transposon Mutation to occur. The default value is 0.

randomAssortment

Random Assortment of Chromosomes for recombinations. The default value is TRUE.

embryonicSelection

Remove chromosomes with fitness < specified value. The default value is NA.

EveryGeneInInitialPopulation

Request for every gene to be present in the initial population. The default value is TRUE.

nnetSize

for nnetI. The default value is NA.

nnetDecay

for nnetI. The default value is NA.

rdaAlpha

for rdaI. The default value is NA.

rdaDelta

for rdaI. The default value is NA.

...

Additional arguments.

Value

The output is a list containing 5 named vectors, records of the evolution:

DGenes

The occurrences in selected genotypes for every gene,

dGenes

The occurrences in discarded genotypes for every gene,

MaximumAccuracy

Maximum accuracy in every generation,

MeanAccuracy

Average accuracy in every generation,

MinAccuracy

Minimum accuracy in every generation,

BestIndividuals

Best individual in every generation.

Examples

## Not run: 
 library(genefilter)
 library(ALL)
 data(ALL)
 bALL = ALL[, substr(ALL$BT,1,1) == "B"]
 smallALL = bALL[, bALL$mol.biol %in% c("BCR/ABL", "NEG")]
 smallALL$mol.biol = factor(smallALL$mol.biol)
 smallALL$BT = factor(smallALL$BT)
 f1 <- pOverA(0.25, log2(100))
 f2 <- function(x) (IQR(x) > 0.5)
 f3 <- ttest(smallALL$mol.biol, p=0.1)
 ff <- filterfun(f1, f2, f3)
 selectedsmallALL <- genefilter(exprs(smallALL), ff)
 smallALL = smallALL[selectedsmallALL, ]
 rm(f1)
 rm(f2)
 rm(f3)
 rm(ff)
 rm(bALL)
 sum(selectedsmallALL)

 set.seed(149)
 res<-dGAselID(smallALL, "mol.biol", trainTest=1:79, startGenes=12, populationSize=200,
               iterations=150, noChr=5, pMutationChance=0.0075, elitism=4)
 
## End(Not run)