Nothing
scoretest <- function(x,y,n.perm=0,pheno.perm=NULL) {
n <- length(y)
if(!ncol(x) == n)
stop("x should have dim p x n, where n is length(y).")
if(n.perm>0)
pheno.perm <- genperms(y,n.perm)
if(!is.null(pheno.perm)) {
if(nrow(pheno.perm) != n)
stop("length of phenotype vector must equal total number of cases and controls.\n")
n.perm <- ncol(pheno.perm)
}
permute <- n.perm > 0
if(!permute) {
return(pchisq(myscore(x,y),df=1,lower.tail=FALSE))
}
result <- matrix(NA,nrow(x),n.perm)
for(i in 1:n.perm) {
cat(".")
result[,i] <- pchisq(myscore(x,pheno.perm[,i]),df=1)
}
return(result)
}
myscore <- function(x,y) { # x is a matrix of explanatory vars, y is a vector of response (0,1)
x <- t(x - rowMeans(x))
U <- colSums(y * x)
n <- length(y)
V <- sum( (y - mean(y))^2 ) * colSums(x^2) / n
X <- U^2/V
return(X)
}
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