Nothing
snpfmridata <-
function(n=300, gamma=0.00001, ncomps=2, jth=1)
{
sig1 <- 0.5
sig2 <- 1
p1 <- 100
p2 <- 100
pt <- 100
a <- rep(0, pt)
a[1:p1] <- ranuf(p1)
b <- rep(0,pt)
b[1:p2] <- ranuf(p2) #using rndu.r file
maf <- runif(pt,0.2, 0.4) # (0,1)/5+0.2 # form uiform distribution
mu <- rnorm(n, 0, 1)
mu <- sign(mu)*(abs(mu)+0.1);# normal distribution add some samll term 0.1
mu <-mu*sig1
ind <- rep(F,pt) #logical(pt) # logical zeors
ind <- as.integer(ind)
ind[1:p2] <- 1 # take 1 1: p2 matrix( rnorm(N*M,mean=0,sd=1), N, M)
m1 <- mu%*%t(a)+matrix(rnorm(n*pt, 0, 1), n, pt)*sig1 #fmri
m2 <- mu%*%t(b)+matrix(rnorm(n*pt, 0, 1), n, pt)*sig2 # SNP
for ( i in 1: pt)
{
p <- maf[i]
bias <- log(1/p-1)
if (ind[i]==TRUE)
{
gt <- m2[,i]
gt <- 1/(1+exp(-gt+bias)) # for correlated variables case
}
else
gt <- 1/(1+exp(bias)) #For no correlated variable #control
temp <- runif(n,0,1)
m2[,i] <- gt > temp
temp <- runif(1, 0,1)
m2[,i] <- m2[,i]+(gt > temp)
}
E3X <- m1
E3Y <- m2
n1 <- (0.05*n)
ss <- sample(1:n, n1)
m1 <-mu[ss]%*%t(a)+matrix(rnorm(n1*pt, 0, 1), n1,pt)*10 #fmri
m2 <- mu[ss]%*%t(b)+matrix(rnorm(n1*pt, 0, 1), n1,pt)*20
for ( i in 1: pt)
{
p <- maf[i]
bias <- log(1/p-1)
if (ind[i]==TRUE)
{
gt <- m2[,i]
gt <- 1/(1+exp(-gt+bias)) # for correlated variables
}
else
gt <- 1/(1+exp(bias)) #For no correlated variable
temp <- runif(n1,0,1)
m2[,i] <- gt > temp
temp <- runif(1, 0,1)
m2[,i] <- m2[,i]+(gt > temp)
}
E3Xot <- rbind(E3X[-ss,],m1)
E3Yot <- rbind(E3Y[-ss,],m2)
CCAID <- ifcca(E3X,E3Y, gamma, ncomps, jth)
CCACD <- ifcca(E3Xot,E3Yot, gamma, ncomps, jth)
KCCAID <- ifrkcca(E3X,E3Y, "square", "linear", gamma, ncomps, jth)
KCCACD <- ifrkcca(E3Xot,E3Yot, "square", "linear", gamma, ncomps, jth)
HARKCCAID <- ifrkcca(E3X, E3Y, "Hampel", "linear", gamma, ncomps, jth)
HARKCCACD <- ifrkcca(E3Xot,E3Yot, "Hampel", "linear",gamma, ncomps, jth)
HURKCCAID <- ifrkcca(E3X,E3Y, "Huber", "linear", gamma, ncomps, jth)
HURKCCACD <- ifrkcca(E3Xot, E3Yot, "Huber", "linear",gamma, ncomps, jth)
CCAIFID <- CCAID$iflccor
CCAIFCD <- CCACD$iflccor
KCCAIFID <- KCCAID$ifrkcor
KCCAIFCD <- KCCACD$ifrkcor
HAKCCAIFID <- HARKCCAID$ifrkcor
HAKCCAIFCD <- HARKCCACD$ifrkcor
HUKCCAIFID <- HURKCCAID$ifrkcor
HUKCCAIFCD <- HURKCCAID$ifrkcor
{
par(mfrow=c(4,2))
par(mar=c(5.1,5.1,4.1,2.1))
plot(CCAIFID, pch=21:22,main=list("Ideal Data",cex =2, font=15), sub=list("Linear CCA",cex =2, font=15),ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
plot(CCAIFCD, pch=21:22, main=list("Contaminated Data",cex =2, font=15),sub=list("Linear CCA",cex =2, font=15), ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
plot(KCCAIFID, pch=21:22, main=list("",cex =2, font=15),sub=list("Kernel CCA",cex =2, font=15),ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
plot(KCCAIFCD, pch=21:22, main=list("",cex =2, font=15),sub=list(" Kernel CCA",cex =2, font=15),ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
plot(HAKCCAIFID, pch=21:22, main=list("",cex =2, font=15), sub=list(" Hampel's robust kernel CCA",cex =2, font=15),ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
plot(HAKCCAIFCD, pch=21:22, main=list("",cex =2, font=15),sub=list(" Hampel's robust kernel CCA",cex =2, font=15), ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
plot(HUKCCAIFID, pch=21:22, main=list("",cex =2, font=15),sub=list(" Huber's robust kernel CCA",cex =2, font=15),ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
plot(HUKCCAIFCD, pch=21:22, main=list("",cex =2, font=15),sub=list(" Huber's robust kernel CCA",cex =2, font=15),ylab="",xlab=list(" ",cex =2, font=15),
type="o",lwd=3,cex.axis=2,cex.lab=2,axes=FALSE)
axis(2, las=0,cex.axis=2,cex.lab=2)
}
return(list(IFCCAID = CCAIFID, IFCCACD = CCAIFCD, IFKCCAID = KCCAIFID, IFKCCACD = KCCAIFCD, IFHAKCCAID = HAKCCAIFID, IFHAKCCACD = HAKCCAIFCD, IFHUKCCAID = HUKCCAIFID, IFHUKCCACD = HUKCCAIFCD))
}
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