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#' Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association.
#'
#' It gives p-values of the SPUpath tests and aSPUpath test.
#'
#' @param Y Response or phenotype data. It can be a disease indicator; =0 for controls, =1 for cases.
#' Or it can be a quantitative trait. A vector with length n (number of observations).
#'
#' @param X Genotype or other data; each row for a subject, and each column
#' for an SNP (or a predictor). The value of each SNP is the # of the copies
#' for an allele. A matrix with dimension n by k (n : number of observation, k : number of SNPs (or predictors) ).
#'
#' @param cov Covariates. A matrix with dimension n by p (n :number of observation, p : number of covariates).
#'
#' @param model Use "gaussian" for a quantitative trait, and use "binomial" for a binary trait.
#'
#' @param snp.info SNP information matrix, the 1st column is SNP id, 2nd column is chromosome #, 3rd column indicates SNP location.
#'
#' @param gene.info GENE information matrix, The 1st column is GENE id, 2nd column is chromosome #, 3rd and 4th column indicate start and end positions of the gene.
#'
#' @param pow SNP specific power(gamma values) used in SPUpath test.
#'
#' @param pow2 GENE specific power(gamma values) used in SPUpath test.
#'
#' @param n.perm number of permutations.
#'
#' @param usePCs indicating whether to extract PCs and then use PCs of X.
#'
#' @param varprop the proportion of the variations explained (cutoff) that
#' determines how many top PCs to use.
#'
#' @return P-values for SPUpath tests and aSPUpath test.
#'
#' @author Il-Youp Kwak and Wei Pan
#'
#' @references
#' Wei Pan, Il-Youp Kwak and Peng Wei (2015)
#' A Powerful and Pathway-Based Adaptive Test for Genetic Association With Common or Rare Variants, The American Journal of Human Genetics, 97, 86-98
#'
#' @examples
#'
#' \dontrun{dat1<-simPathAR1Snp(nGenes=20, nGenes1=5, nSNPlim=c(1, 20),
#' nSNP0=1, LOR=.2, n=100, MAFlim=c(0.05, 0.4), p0=0.05 ) }
#' \dontshow{dat1<-simPathAR1Snp(nGenes=20, nGenes1=5, nSNPlim=c(1, 20),
#' nSNP0=1, LOR=.2, n=5, MAFlim=c(0.05, 0.4), p0=0.05 ) }
#'
#' # p-values of SPUpath and aSPUpath tests.
#' \dontrun{p.pathaspu<- aSPUpath(dat1$Y, dat1$X, snp.info = dat1$snp.info,
#' gene.info = dat1$gene.info,
#' model = "binomial", pow=1:8, pow2=c(1, 2, 4, 8), n.perm=1000) }
#' \dontshow{p.pathaspu<- aSPUpath(dat1$Y, dat1$X, snp.info = dat1$snp.info,
#' gene.info = dat1$gene.info,
#' model = "binomial", pow=1:8, pow2=c(1, 2, 4, 8), n.perm=3) }
#' p.pathaspu
#' ## pow = 1:8 and pow2 = 1,2,4,8
#' ## So, there are 8*4 = 32 SPUpath p-values.
#' ## SPUpathi,j corresponds pow = i , pow2 = j
#' ## The last element, aSPUpath gives aSPUpath p-value.
#'
#' @seealso \code{\link{simPathAR1Snp}}
#'
#' @export
aSPUpath <- function(Y, X, cov = NULL, model=c("binomial", "gaussian"),
snp.info, gene.info, pow=c(1:8, Inf), pow2=c(1,2,4,8),
n.perm=200, usePCs=F, varprop=0.95 ){
model = match.arg(model)
## some input checking stuff in here
if( any(is.na(X)) ) {
stop("NA exist in gene matrix. ")
}
if( any(is.na(Y)) ) {
stop("NA exist in phenotype. ")
}
n.gene <- nrow(gene.info)
GL <- list(0)
i = 1
for(g in 1:n.gene) { # g = 2
snpTF <- ( snp.info[,2] == gene.info[g,2] &
gene.info[g,3] <= as.numeric(snp.info[,3]) &
gene.info[g,4] >= as.numeric(snp.info[,3]) )
if( sum(snpTF) != 0){
GL[[i]] <- which(snpTF)
i = i + 1
}
}
X = X[, unlist(GL)]
nSNPs=unlist(lapply(GL,length))
nSNPs0<-rep(0, length(nSNPs))
if (usePCs){
Xg<-NULL
for(iGene in 1:length(nSNPs)){
if (iGene==1) SNPstart=1 else SNPstart=sum(nSNPs[1:(iGene-1)])+1
indx=(SNPstart:(SNPstart+nSNPs[iGene]-1))
Xpcs<-extractPCs(X[, indx], cutoff=varprop)
Xg<-cbind(Xg, Xpcs)
if (is.null(ncol(Xpcs))) nSNPs0[iGene]=1
else nSNPs0[iGene]=ncol(Xpcs)
}
} else { Xg=X; nSNPs0=nSNPs}
n<-length(Y)
k<-ncol(Xg)
#######construction of the score vector:
if (is.null(cov)){
## NO nuisance parameters:
XUs<-Xg
r<-Y-mean(Y)
U<-as.vector(t(Xg) %*% r)
} else {
tdat1<-data.frame(trait=Y, cov)
if(is.null(colnames(cov))) {
colnames(tdat1) = c("trait", paste("cov",1:dim(cov)[2],sep=""))
} else {
colnames(tdat1) = c("trait", colnames(cov))
}
fit1<-glm(trait~.,family=model,data=tdat1)
pis<-fitted.values(fit1)
XUs<-matrix(0, nrow=n, ncol=k)
Xmus = Xg
for(i in 1:k){
tdat2<-data.frame(X1=X[,i], cov)
fit2<-glm(X1~.,data=tdat2)
Xmus[,i]<-fitted.values(fit2)
XUs[, i]<-(X[,i] - Xmus[,i])
}
r<-Y - pis
U<-t(XUs) %*% r
}
nGenes=length(nSNPs0)
## test stat's:
StdTs<-rep(0, length(pow)*nGenes)
for(j in 1:length(pow))
for(iGene in 1:nGenes){
if (iGene==1) SNPstart=1 else SNPstart=sum(nSNPs0[1:(iGene-1)])+1
indx=(SNPstart:(SNPstart+nSNPs0[iGene]-1))
if (pow[j] < Inf){
a= (sum(U[indx]^pow[j]))
StdTs[(j-1)*nGenes+iGene] = sign(a)*((abs(a)/nSNPs0[iGene]) ^(1/pow[j]))
} else {
StdTs[(j-1)*nGenes+iGene] =max(abs(U[indx]))
}
}
## Permutations:
StdT0s = matrix(0, nrow=n.perm, ncol=length(pow)*nGenes)
for(b in 1:n.perm){
R0 <- sample(r, length(r))
#########Null score vector:
U0<-t(XUs) %*% R0
## test stat's:
for(j in 1:length(pow))
for(iGene in 1:nGenes){
if (iGene==1) SNPstart=1 else SNPstart=sum(nSNPs0[1:(iGene-1)])+1
indx=(SNPstart:(SNPstart+nSNPs0[iGene]-1))
if (pow[j] < Inf){
a = (sum(U0[indx]^pow[j]))
StdT0s[b, (j-1)*nGenes+iGene] = sign(a)*((abs(a)/nSNPs0[iGene]) ^(1/pow[j]))
} else StdT0s[b, (j-1)*nGenes+iGene] = max(abs(U0[indx]))
}
}
#combine gene-level stats to obtain pathway-lelev stats:
Ts2<-rep(0, length(pow)*length(pow2))
T0s2<-matrix(0, nrow=n.perm, ncol=length(pow)*length(pow2))
for(j2 in 1:length(pow2)){
for(j in 1:length(pow)){
if(pow2[j2] < Inf) {
Ts2[(j2-1)*length(pow) +j] = sum(StdTs[((j-1)*nGenes+1):(j*nGenes)]^pow2[j2])
for(b in 1:n.perm){
T0s2[b, (j2-1)*length(pow) +j] = sum(StdT0s[b, ((j-1)*nGenes+1):(j*nGenes)]^pow2[j2])
}
} else {
Ts2[(j2-1)*length(pow) +j] =
max(StdTs[((j-1)*nGenes+1):(j*nGenes)])
for(b in 1:n.perm){
T0s2[b, (j2-1)*length(pow) +j] = max(StdT0s[b, ((j-1)*nGenes+1):(j*nGenes)])
}
}
}
}
# permutation-based p-values:
pPerm2 = rep(NA, length(pow)*length(pow2));
pvs = NULL;
for(j in 1:(length(pow)*length(pow2))) {
pPerm2[j] = sum( abs(Ts2[j]) < abs(T0s2[,j]))/n.perm
}
P0s2 = PermPvs(T0s2)
minP0s2 = apply(P0s2, 1, min)
minP2 = sum( min(pPerm2) > minP0s2 )/n.perm
minP1s<-minP2s<-minPUs<-rep(NA, length(pow2))
pvs=c(pPerm2, minP2)
nmvec <- NULL;
for(ii in pow2) {
for(jj in pow) {
nmvec <- c(nmvec, paste("SPUMpath",jj,",",ii,sep=""))
}
}
nmvec <- c(nmvec, "aSPUpath")
names(pvs) <- nmvec
pvs
}
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