dim(my.gini.perm)
load("my.data.selected.imputed.RData")
load("my.gini.perm.RData")
nlevelsSNPs<-sapply(my.data.selected.imputed[,-1],FUN=function(x) nlevels(factor(x)))
my.snps2<-my.data.selected.imputed[,1+which(nlevelsSNPs==2)]
my.gini.perm2<-my.importance[which(nlevelsSNPs==2),]
my.data.selected.imputed[1:5,]
my.data.selected.imputed[1:5,1:5]
nlevelsSNPs
my.snps2<-my.data.selected.imputed[,1+which(nlevelsSNPs==2)]
my.gini.perm2<-my.gini.perm[which(nlevelsSNPs==2),]
freq2<-function(x)
{
tab<-table(x)
return(min(tab)/sum(tab))
}
my.freq2<-sapply(my.snps2,FUN=freq2)
my.snps3<-my.data.selected.imputed[,1+which(nlevelsSNPs==3)]
my.gini.perm3<-my.gini.perm[which(nlevelsSNPs==3),]
maf3<-function(x)
{
tab<-table(x)
return((tab[2]+2*min(tab[1],tab[3]))/(2*sum(tab)))
}
my.maf3<-sapply(my.snps3,FUN=maf3)
boxplot(as.numeric(my.gini.perm3[my.maf3<0.1,]))
boxplot(as.numeric(my.gini.perm3[my.maf3<0.1,]),as.numeric(my.gini.perm3[my.maf3>=0.1&my.maf3<0.2,]),as.numeric(my.gini.perm3[my.maf3>=0.2&my.maf3<0.3,]),as.numeric(my.gini.perm3[my.maf3>=0.3& my.maf3<0.4,]),as.numeric(my.gini.perm3[my.maf3>=0.4,]),ylim=c(0,0.1))
load("my.perm.perm.RData")
my.perm.perm2<-my.perm.perm[which(nlevelsSNPs==2),]
my.perm.perm3<-my.perm.perm[which(nlevelsSNPs==3),]
boxplot(as.numeric(my.perm.perm3[my.maf3<0.1,]),as.numeric(my.perm.perm3[my.maf3>=0.1&my.maf3<0.2,]),as.numeric(my.perm.perm3[my.maf3>=0.2&my.maf3<0.3,]),as.numeric(my.perm.perm3[my.maf3>=0.3& my.maf3<0.4,]),as.numeric(my.perm.perm3[my.maf3>=0.4,]),ylim=c(0,0.1))
my.perm.perm3
boxplot(as.numeric(my.perm.perm3[my.maf3<0.1,]),as.numeric(my.perm.perm3[my.maf3>=0.1&my.maf3<0.2,]),as.numeric(my.perm.perm3[my.maf3>=0.2&my.maf3<0.3,]),as.numeric(my.perm.perm3[my.maf3>=0.3& my.maf3<0.4,]),as.numeric(my.perm.perm3[my.maf3>=0.4,]),ylim=c(0,1e-5))
boxplot(as.numeric(my.perm.perm3[my.maf3<0.1,]),as.numeric(my.perm.perm3[my.maf3>=0.1&my.maf3<0.2,]),as.numeric(my.perm.perm3[my.maf3>=0.2&my.maf3<0.3,]),as.numeric(my.perm.perm3[my.maf3>=0.3& my.maf3<0.4,]),as.numeric(my.perm.perm3[my.maf3>=0.4,]),ylim=c(-5e-5,5e-5))
