Proxy External Controls Association Test
rare-variant genetic region association test to robustly use publicly available data with allele frequencies in case-control analysis.
Notes: --We have found better results by using fairly stringent internal minor allele frequency filters of 1% or 0.1% in either cases or in controls --make sure to use cases and controls matched by ancestral population
To install in R, (1) install the package devtools (2) library(devtools) (3) install_github("hendriau/ProxECAT")
To run proxecat or proxecat_over in R,
proxecat::proxecat(x1, x2, x3, x4)
proxecat::proxecat_over(x1, x2, x3, x4, size=1000)
where x1 is a vector of the number of functional rare alleles in cases for each gene region
x2 is a vector of the number of synonymous rare alleles (or other proxy) in cases for each gene region
x3 is a vector of the number of functional rare alleles in controls for each gene region
x4 is a vector of the number of synonymous rare alleles (or other proxy) in controls for each gene region
size is the overdispersion parameter. The smaller size, the more over dispersed. The larger size the less overdispersed. Size of >1000 is approximately Poisson.
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