Nothing
filter.ambig.snps <- function(sum.stat, allele.info, options){
msg <- paste("Removing SNPs with ambiguous alleles and missing allele frequency:", date())
if (options$print) message(msg)
exc.snps <- NULL
sum.info <- sum.stat$stat
nstudy <- length(sum.info)
ref <- allele.info[, 'RefAllele']
eff <- allele.info[, 'EffectAllele']
tmp <- ambig.snps(ref, eff)
if (any(tmp)) {
ambig <- (allele.info$SNP)[tmp]
for (k in 1:nstudy){
dat <- sum.info[[k]]
vec <- as.numeric(dat[, "EAF"])
tmp <- (dat[, "SNP"] %in% ambig) & ( (!is.finite(vec)) | (vec < 0) | (vec > 1) )
tmp[is.na(tmp)] <- TRUE
if (any(tmp)) exc.snps <- c(exc.snps, dat[tmp, "SNP"])
}
exc.snps <- unique(exc.snps)
}
exc.snps
}
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