extract.conflictive.snps <- function(stat, ref.allele){
msg <- paste("Extracting SNPs with conflictive alleles:", date())
message(msg)
RefAllele <- ref.allele$RefAllele
EffectAllele <- ref.allele$EffectAllele
snps <- names(RefAllele)
A1 <- paste(RefAllele, EffectAllele, sep = '')
A2 <- paste(EffectAllele, RefAllele, sep = '')
names(A1) <- snps
names(A2) <- snps
nstudy <- length(stat)
conf.snps <- NULL
for(i in 1:nstudy){
a <- paste(stat[[i]][, 'RefAllele'], stat[[i]][, 'EffectAllele'], sep = '')
s <- stat[[i]][, 'SNP']
names(a) <- s
b <- which(a != A1[s] & a != A2[s])
if(length(b) == 0){
next
}
conf.snps <- c(conf.snps, names(b))
}
conf.snps <- unique(conf.snps)
conf.snps
}
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