aSPU (version 1.50)

GATES2: 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).

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

See Also

Hyst GatesSimes

Examples

# NOT RUN {
#simula <- simPathAR1Snp(nGenes=20, nGenes1=1, nSNPlim=c(1, 20), nSNP0=1:3,
#                           LOR=.2, rholim=c(0,0),
#                           n=30, MAFlim=c(0.05, 0.4), p0=0.05)
#Ps <- getlogitp(simula$Y, simula$X)

## get correlation of SNPs using controls
#ldmat <- cor(simula$X[ simula$Y == 0, ])

#o.pvec = order(Ps)
# ldmat <- ldmat[o.pvec, o.pvec]
#(gatesp <- GATES2(ldmat, sort(Ps))[1])


# }