extract.reference.allele <- function(stat){
msg <- paste("Extracting allele information:", date())
message(msg)
snps <- NULL
nstudy <- length(stat)
for(i in 1:nstudy){
snps <- unique(c(snps, stat[[i]][, 'SNP']))
}
nsnp <- length(snps)
RefAllele <- rep(NA, nsnp)
EffectAllele <- rep(NA, nsnp)
names(RefAllele) <- snps
names(EffectAllele) <- snps
# use the same strategy as in recover.stat() to determine which allele is used as the reference allele when merging data or creating scores from multiple studies
for(i in 1:nstudy){
s <- stat[[i]][, 'SNP']
if(any(is.na(RefAllele[s]))){
s <- s[is.na(RefAllele[s])]
RefAllele[s] <- stat[[i]][s, 'RefAllele']
}
s <- stat[[i]][, 'SNP']
if(any(is.na(EffectAllele[s]))){
s <- s[is.na(EffectAllele[s])]
EffectAllele[s] <- stat[[i]][s, 'EffectAllele']
}
}
list(RefAllele = RefAllele, EffectAllele = EffectAllele)
}
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