dGAselID (version 1.2)

EmbryonicSelection: EmbryonicSelection

Description

Function for deleting individuals with a fitness below a specified threshold.

Usage

EmbryonicSelection(population, results, embryonicSelection)

Arguments

population

Population of individuals with diploid genotypes.

results

Results returned by EvaluationFunction().

embryonicSelection

Threshold value. The default value is NA.

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(1357)

 population0<-InitialPopulation(smallALL, 14, 8, FALSE)
 individuals0<-Individuals(population0)
 results0<-EvaluationFunction(smallALL, individuals0, response="mol.biol",
             method=knn.cvI(k=3, l=2), trainTest="LOG")
 EmbryonicSelection(individuals0, results0, 0.5)
 
# }