R: Gene-based Association Test that uses an extended Simes...
GATES2
R Documentation
Gene-based Association Test that uses an extended Simes procedure (GATES) for single trait - SNP set association
Description
Get the p-value of GATES. Usually it is used to get genomewise p-values.
This function is taken from postgwas package.
There is a little modification of the code GATES in postgwas package.
1) The approximated matrix may have negative eigen value, we modified it not to have negative values; 2) we added one more return (the key gene location) for Hyst method.
Usage
GATES2(ldmatrix, p)
Arguments
ldmatrix
numeric. A correlation matrix of SNPs,
dimensions matching the p and snps arguments.
p
p-value for each SNPs.
Value
A p-value of GATES and the key gene location (to be used by Hyst).
Author(s)
Milan Hiersche(taken from pastgwas package), Il-Youp Kwak(modified a little)
References
Miao-Xin Li, Hong-Sheng Gui, Johnny S.H. Kwan and Pak C. Sham (2011)
GATES: A Rapid and Powerful Gene-Based Association Test Using Extended Simes Procedure
The American Journal of Human Genetics 88, 283-293