Allele Frequency Comparison
Description
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) .