Nothing
lme.EC <- function(snp,phen,test.dat,covar,kmat=kmat,chr){
maf.fun <- function(x){
if (all(is.na(x))) maf <- NA else {
x <- na.omit(x)
maf <- (sum(x==1)+sum(x==2)*2)/(2*length(x))
maf <- ifelse(maf<0.5,maf,1-maf)
}
maf
}
maf.fun.x <- function(x,sex){
if (all(is.na(x))) maf <- NA else {
x <- na.omit(cbind(x,sex))
maf <- (sum(x[x[,2]==2,1])+sum(x[x[,2]==1,1])/2)/(2*sum(x[,2]==2)+sum(x[,2]==1))
maf <- ifelse(maf<0.5,maf,1-maf)
}
maf
}
cor.snp <- function(y,x){
return(sd(y)==0 || abs(cor(y,x,use="complete"))>0.99999999 )
}
na.ind <- if (missing(covar)) !is.na(snp) & !is.na(test.dat[,phen]) else
if (length(covar)>1) !is.na(snp) & !is.na(test.dat[,phen]) & apply(!is.na(test.dat[,covar]),1,all) else
!is.na(snp) & !is.na(test.dat[,phen]) & !is.na(test.dat[,covar])
snp1=snp[na.ind]; sex=test.dat[na.ind,"sex.in.ped"]
phen1=test.dat[na.ind,phen]; id=test.dat[na.ind,"id"]
if (!missing(covar)) x.covar <- as.matrix(test.dat[na.ind,covar])
###########################################
count <- table(snp1)
gntps <- names(count)
count1 <- rep(0,3)
count1[as.numeric(gntps)+1] <- count
if (count1[1]>count1[3]) MAC <- count1[2]+count1[3]*2 else MAC <- count1[2]+2*count1[1]
ntotal <- sum(count)
nmiss <- length(snp)-ntotal
if (chr=="X") maf_ntotal <- maf.fun.x(snp1,sex) else maf_ntotal <- maf.fun(snp1)
###########################################
if (length(unique(phen1))<=1 ) {
lme.out= list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"single category in phen",NA,MAC,count1[1],count1[2],count1[3])
return(lme.out)
}
###########################################
if (length(count)==1 ) {
lme.out <- list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"single category in SNP",NA,MAC,count1[1],count1[2],count1[3])
return(lme.out)
}
###########################################
if (length(unique(snp1))>1 && !missing(covar)){
if (length(covar)>1) colinear <- apply(x.covar,2,cor.snp,x=snp1) else colinear <- cor.snp(x.covar,snp1)
if (sum(colinear)>0){
lme.out= list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"collinarity",NA,MAC,count1[1],count1[2],count1[3])
return(lme.out)
}
}
#############################################
# Perform LME
#############################################
if (!missing(covar)) lme.test <- try(lmekin(phen1 ~ snp1+x.covar+(1|id),varlist=kmat)) else lme.test <- try(lmekin(phen1 ~ snp1+(1|id),varlist=kmat))
if (!"try-error" %in% class(lme.test)){
Z <- lme.test$coef$fixed[2]/sqrt(lme.test$var[2,2])
lme.out <- list(ntotal,nmiss,maf_ntotal,lme.test$coef$fixed[2],sqrt(lme.test$var[2,2]),Z,NA,pchisq(Z^2,1,lower.tail=F),MAC,count1[1],count1[2],count1[3])
} else lme.out= list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"try-error",NA,MAC,count1[1],count1[2],count1[3])
return(lme.out)
}
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