Nothing
filter.conflictive.snps <- function(sum.stat, allele.info, options){
msg <- paste("Removing SNPs with conflictive allele information:", date())
if(options$print) message(msg)
sum.info <- sum.stat$stat
nstudy <- length(sum.info)
foo <- function(x){
paste(sort(x), collapse = '')
}
ref.allele <- apply(allele.info[, c('RefAllele', 'EffectAllele')], 1, foo)
names(ref.allele) <- allele.info$SNP
exc.snps <- NULL
for(k in 1:nstudy){
ord.allele <- apply(sum.info[[k]][, c('RefAllele', 'EffectAllele')], 1, foo)
rs <- names(ord.allele)
id <- which(ord.allele != ref.allele[rs])
if(length(id) > 0){
exc.snps <- c(exc.snps, rs[id])
}
}
exc.snps <- unique(exc.snps)
exc.snps
}
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