Allele Frequency Comparison
When doing association analysis one does not always have the genotypes for the control population. In such cases it may be necessary to fall back on frequency based tests using well known sources for the frequencies in the control population, for instance, from the 1000 Genomes Project. The Allele Frequency Comparison ('AssocAFC') package performs multiple rare variant association analyses in both population and family-based GWAS (Genome-Wide Association Study) designs. It includes three score tests that are based on the difference of the sum of allele frequencies between cases and controls. Two of these tests, Wcorrected() and Wqls(), are collapsing-based tests and suffer from having protective and risk variants. The third test, afcSKAT(), is a score test that overcomes the mix of SNP (Single-Nucleotide Polymorphism) effect directions. For more details see Saad M and Wijsman EM (2017) <doi:10.1093/bib/bbx107>.