In this paper, 3000+ subjects were genotyped by two/three different chips. They used Mantel extension test to identify high discrepancy allele frequency of SNPs, which may due to chip/batch effect, e.g 0.30 in chip A, 0.21 in chip B, 0.35 in chip C.

Or even for the same chip but genotyped in different time, there might be some different in allele frequency. I need to check the similarity of the genotypes before association analysis. Otherwise, it may cause false positive results.

I don't have strong math background. Although I have read some materials introducing CMH test, I don't know how to generate a matrix that can be used for mantel extension test in R.

Is there anyone that can help and give me an example?

Thanks.