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NormalizationEffect <-
function(MaxOrder,SingleEffect,TwoEffect,ThreeEffect,
FourEffect,FiveEffect,SaveFileName=""){
# Normalization of SingleEffect, TwoEffect, ThreeEffect, FourEffect and FiveEffect
#
# input
# MaxOrder: the specified maximum order, must be setted as 1,2,3,4 or 5.
# SingleEffect: There are 2 columns. The first column saves all SNPs, and the
# second column saves their corresponding effects. Descending
# save according to their effects.
# TwoEffect: There are 3 columns. The first 2 columns save all 2-SNP combinations,
# and the last column saves their corresponding effects. Descending
# save according to their interaction effects.
# ThreeEffect: There are 4 columns. The first 3 columns save all 3-SNP combinations,
# and the last column saves their corresponding effects. Descending
# save according to their interaction effects.
# FourEffect: There are 5 columns. The first 4 columns save all 4-SNP combinations,
# and the last column saves their corresponding effects. Descending
# save according to their interaction effects.
# FiveEffect: There are 6 columns. The first 5 columns save all 5-SNP combinations,
# and the last column saves their corresponding effects. Descending
# save according to their interaction effects.
# SaveFileName: basic file name for saving figure.
#
# output
# SingleEffect: The normalization of SingleEffect
# TwoEffect: The normalization of TwoEffect
# ThreeEffect: The normalization of ThreeEffect
# FourEffect: The normalization of FourEffect
# FiveEffect: The normalization of FiveEffect
#
# Junliang Shang
# 4.6/2014
if(MaxOrder==2){
meanSingle <- mean(SingleEffect[,2])
meanTwo <- mean(TwoEffect[,3])
rowSingle <- nrow(SingleEffect)
rowTwo <- nrow(TwoEffect)
x <- seq(1, rowSingle+rowTwo)
y <- c(SingleEffect[,2],TwoEffect[,3])
SingleEffect[,2] <- SingleEffect[,2]*meanTwo/meanSingle
z <- c(SingleEffect[,2],TwoEffect[,3])
NmeanSingle <- mean(SingleEffect[,2])
NmeanTwo <- meanTwo
# plot
x.pch <- rep(5,length(x))
x.pch[1:rowSingle] <- 1
x.col <- rep("red",length(x))
x.col[1:rowSingle] <- "green"
dev.new()
set.seed(8)
layout(matrix(1:2, 2, 1))
plot(log(x),y,pch=x.pch,col=x.col,xlab=NA,ylab="Original Effect")
lines(log(1:rowSingle),rep(meanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(meanTwo,rowTwo),col="red")
plot(log(x),z,pch=x.pch,col=x.col,xlab=NA,ylab="Normalized Effect")
lines(log(1:rowSingle),rep(NmeanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(NmeanTwo,rowTwo),col="red")
# savePlot(filename=paste(SaveFileName,"_N",sep=""),type="tiff")
}
if(MaxOrder==3){
meanSingle <- mean(SingleEffect[,2])
meanTwo <- mean(TwoEffect[,3])
meanThree <- mean(ThreeEffect[,4])
rowSingle <- nrow(SingleEffect)
rowTwo <- nrow(TwoEffect)
rowThree <- nrow(ThreeEffect)
x <- seq(1, rowSingle+rowTwo+rowThree)
y <- c(SingleEffect[,2],TwoEffect[,3],ThreeEffect[,4])
SingleEffect[,2] <- SingleEffect[,2]*meanTwo/meanSingle
ThreeEffect[,4] <- ThreeEffect[,4]*meanTwo/meanThree
z <- c(SingleEffect[,2],TwoEffect[,3],ThreeEffect[,4])
NmeanSingle <- mean(SingleEffect[,2])
NmeanTwo <- meanTwo
NmeanThree <- mean(ThreeEffect[,4])
# plot
x.pch <- rep(5,length(x))
x.pch[1:rowSingle] <- 1
x.pch[(rowSingle+1):(rowSingle+rowTwo)] <- 2
x.col <- rep("red",length(x))
x.col[1:rowSingle] <- "green"
x.col[(rowSingle+1):(rowSingle+rowTwo)] <- "blue"
dev.new()
set.seed(8)
layout(matrix(1:2, 2, 1))
plot(log(x),y,pch=x.pch,col=x.col,xlab=NA,ylab="Original Effect")
lines(log(1:rowSingle),rep(meanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(meanTwo,rowTwo),col="blue")
lines(log((rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)),
rep(meanThree,rowThree),col="red")
plot(log(x),z,pch=x.pch,col=x.col,xlab=NA,ylab="Normalized Effect")
lines(log(1:rowSingle),rep(NmeanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(NmeanTwo,rowTwo),col="blue")
lines(log((rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)),
rep(NmeanThree,rowThree),col="red")
# savePlot(filename=paste(SaveFileName,"_N",sep=""),type="tiff")
}
if(MaxOrder==4){
meanSingle <- mean(SingleEffect[,2])
meanTwo <- mean(TwoEffect[,3])
meanThree <- mean(ThreeEffect[,4])
meanFour <- mean(FourEffect[,5])
rowSingle <- nrow(SingleEffect)
rowTwo <- nrow(TwoEffect)
rowThree <- nrow(ThreeEffect)
rowFour <- nrow(FourEffect)
x <- seq(1, rowSingle+rowTwo+rowThree+rowFour)
y <- c(SingleEffect[,2],TwoEffect[,3],ThreeEffect[,4],FourEffect[,5])
SingleEffect[,2] <- SingleEffect[,2]*meanTwo/meanSingle
ThreeEffect[,4] <- ThreeEffect[,4]*meanTwo/meanThree
FourEffect[,5] <- FourEffect[,5]*meanTwo/meanFour
z <- c(SingleEffect[,2],TwoEffect[,3],ThreeEffect[,4],FourEffect[,5])
NmeanSingle <- mean(SingleEffect[,2])
NmeanTwo <- meanTwo
NmeanThree <- mean(ThreeEffect[,4])
NmeanFour <- mean(FourEffect[,5])
# plot
x.pch <- rep(5,length(x))
x.pch[1:rowSingle] <- 1
x.pch[(rowSingle+1):(rowSingle+rowTwo)] <- 2
x.pch[(rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)] <- 3
x.col <- rep("red",length(x))
x.col[1:rowSingle] <- "green"
x.col[(rowSingle+1):(rowSingle+rowTwo)] <- "blue"
x.col[(rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)] <- "cyan"
dev.new()
set.seed(8)
layout(matrix(1:2, 2, 1))
plot(log(x),y,pch=x.pch,col=x.col,xlab=NA,ylab="Original Effect")
lines(log(1:rowSingle),rep(meanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(meanTwo,rowTwo),col="blue")
lines(log((rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)),
rep(meanThree,rowThree),col="cyan")
lines(log((rowSingle+rowTwo+rowThree+1):(rowSingle+rowTwo+rowThree+rowFour)),
rep(meanFour,rowFour),col="red")
plot(log(x),z,pch=x.pch,col=x.col,xlab=NA,ylab="Normalized Effect")
lines(log(1:rowSingle),rep(NmeanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(NmeanTwo,rowTwo),col="blue")
lines(log((rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)),
rep(NmeanThree,rowThree),col="cyan")
lines(log((rowSingle+rowTwo+rowThree+1):(rowSingle+rowTwo+rowThree+rowFour)),
rep(NmeanFour,rowFour),col="red")
# savePlot(filename=paste(SaveFileName,"_N",sep=""),type="tiff")
}
if(MaxOrder==5){
meanSingle <- mean(SingleEffect[,2])
meanTwo <- mean(TwoEffect[,3])
meanThree <- mean(ThreeEffect[,4])
meanFour <- mean(FourEffect[,5])
meanFive <- mean(FiveEffect[,6])
rowSingle <- nrow(SingleEffect)
rowTwo <- nrow(TwoEffect)
rowThree <- nrow(ThreeEffect)
rowFour <- nrow(FourEffect)
rowFive <- nrow(FiveEffect)
x <- seq(1, rowSingle+rowTwo+rowThree+rowFour+rowFive)
y <- c(SingleEffect[,2],TwoEffect[,3],ThreeEffect[,4],FourEffect[,5],FiveEffect[,6])
SingleEffect[,2] <- SingleEffect[,2]*meanTwo/meanSingle
ThreeEffect[,4] <- ThreeEffect[,4]*meanTwo/meanThree
FourEffect[,5] <- FourEffect[,5]*meanTwo/meanFour
FiveEffect[,6] <- FiveEffect[,6]*meanTwo/meanFive
z <- c(SingleEffect[,2],TwoEffect[,3],ThreeEffect[,4],FourEffect[,5],FiveEffect[,6])
NmeanSingle <- mean(SingleEffect[,2])
NmeanTwo <- meanTwo
NmeanThree <- mean(ThreeEffect[,4])
NmeanFour <- mean(FourEffect[,5])
NmeanFive <- mean(FiveEffect[,6])
# plot
x.pch <- rep(5,length(x))
x.pch[1:rowSingle] <- 1
x.pch[(rowSingle+1):(rowSingle+rowTwo)] <- 2
x.pch[(rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)] <- 3
x.pch[(rowSingle+rowTwo+rowThree+1):(rowSingle+rowTwo+rowThree+rowFour)] <- 4
x.col <- rep("red",length(x))
x.col[1:rowSingle] <- "green"
x.col[(rowSingle+1):(rowSingle+rowTwo)] <- "blue"
x.col[(rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)] <- "cyan"
x.col[(rowSingle+rowTwo+rowThree+1):(rowSingle+rowTwo+rowThree+rowFour)] <- "black"
dev.new()
set.seed(8)
layout(matrix(1:2, 2, 1))
plot(log(x),y,pch=x.pch,col=x.col,xlab=NA,ylab="Original Effect")
lines(log(1:rowSingle),rep(meanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(meanTwo,rowTwo),col="blue")
lines(log((rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)),
rep(meanThree,rowThree),col="cyan")
lines(log((rowSingle+rowTwo+rowThree+1):(rowSingle+rowTwo+rowThree+rowFour)),
rep(meanFour,rowFour),col="black")
lines(log((rowSingle+rowTwo+rowThree+rowFour+1):(rowSingle+rowTwo+rowThree+rowFour+rowFive)),
rep(meanFive,rowFive),col="red")
plot(log(x),z,pch=x.pch,col=x.col,xlab=NA,ylab="Normalized Effect")
lines(log(1:rowSingle),rep(NmeanSingle,rowSingle),col="green")
lines(log((rowSingle+1):(rowSingle+rowTwo)),rep(NmeanTwo,rowTwo),col="blue")
lines(log((rowSingle+rowTwo+1):(rowSingle+rowTwo+rowThree)),
rep(NmeanThree,rowThree),col="cyan")
lines(log((rowSingle+rowTwo+rowThree+1):(rowSingle+rowTwo+rowThree+rowFour)),
rep(NmeanFour,rowFour),col="black")
lines(log((rowSingle+rowTwo+rowThree+rowFour+1):(rowSingle+rowTwo+rowThree+rowFour+rowFive)),
rep(NmeanFive,rowFive),col="red")
# savePlot(filename=paste(SaveFileName,"_N",sep=""),type="tiff")
}
list(SingleEffect=SingleEffect,TwoEffect=TwoEffect,ThreeEffect=ThreeEffect,
FourEffect=FourEffect,FiveEffect=FiveEffect)
}
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