Nothing
glmm.EC <- function(snp,phen,test.dat,covar,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]; famid=test.dat[na.ind,"famid"]
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 | length(unique(phen1))>2) {
glmm.out <- list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"single category in phen",NA,MAC,count1[1],count1[2],count1[3])
return(glmm.out)
}
###########################################
if (length(count)==1 ) {
glmm.out <- list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"single category in SNP",NA,MAC,count1[1],count1[2],count1[3])
return(glmm.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){
glmm.out= list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"collinarity",NA,MAC,count1[1],count1[2],count1[3])
return(glmm.out)
}
}
#############################################################################################
#
# Perform GLMM
#
#############################################################################################
if (!missing(covar)){
gee.test.0 <- try(glmer(phen1 ~ x.covar+(1|famid), family="binomial",control=glmerControl(optimizer="bobyqa")))
gee.test <- try(glmer(phen1 ~ snp1+x.covar+(1|famid), family="binomial",control=glmerControl(optimizer="bobyqa")))
} else {
gee.test.0 <- try(glmer(phen1 ~ (1|famid), family="binomial",control=glmerControl(optimizer="bobyqa")))
gee.test <- try(glmer(phen1 ~ snp1+(1|famid), family="binomial",control=glmerControl(optimizer="bobyqa")))
}
if (!"try-error" %in% class(gee.test.0) && !"try-error" %in% class(gee.test)){
conv <- is.null(unlist(gee.test@optinfo$conv$lme4)) | (!is.null(unlist(gee.test@optinfo$conv$lme4)) && gee.test@optinfo$conv$lme4$code==0)
if (is.null(unlist(gee.test@optinfo$warnings)) & conv & gee.test@optinfo$conv$opt==0) warning <- NA else warning <- "converging issue"
lrt <- -2*(logLik(gee.test.0)-logLik(gee.test))[1]
gee.test.s <- try(summary(gee.test))
if (!"try-error" %in% class(gee.test.s)){
if (lrt>0) Z <- sign(coef(gee.test.s)["snp1",1])*sqrt(lrt) else Z <- 0
p <- pchisq(lrt,1,lower.tail=F)
glmm.out <- list(ntotal,nmiss,maf_ntotal,coef(gee.test.s)["snp1",1],coef(gee.test.s)["snp1",2],Z,warning,p,MAC,count1[1],count1[2],count1[3])
} else glmm.out= list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"try-error",NA,MAC,count1[1],count1[2],count1[3])
} else glmm.out= list(ntotal,nmiss,maf_ntotal, NA, NA, NA,"try-error",NA,MAC,count1[1],count1[2],count1[3])
return(glmm.out)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.