dGAselID (version 1.0)

dGAselID: dGAselID

Description

Initializes and starts the search with the genetic algorithm.

Usage

dGAselID(x, response, method = knnI(k = 3, l = 2), trainTest = "LOG",
  startGenes, populationSize, iterations, noChr = 22, elitism = NA,
  ID = "ID1", pMutationChance = NA, 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 knnI(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

Incomplete Dominance. The default value is "ID1". Use "ID2" for elitism applied to individuals.

pMutationChance

Chance for a point mutation to occur.

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.

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, 9)
#  f2 <- function(x) (IQR(x) > 0.75)
#  f3 <- ttest(smallALL$mol.biol, p=0.1)
#  ff <- filterfun(f1, f2, f3)
#  selectedsmallALL <- genefilter(exprs(smallALL), ff)
#  sum(selectedsmallALL)
# 
#  set.seed(1357)
#  res1<-dGAselID(smallALL, "mol.biol", method=knn.cvI(k=3, l=2), trainTest=1:79,
#    startGenes=5, populationSize=50, iterations=4, noChr=5, mutationChance=0.05,
#    elitism=10, ID="ID1")
#  
## ---------------------------------------------