SATS: SNP-set association tests using GWAS Summary data

In baolinwu/mkatr: Miscellaneous variant-set association test methods

Description

Compute p-values for the SNP-set tests using GWAS Z-statistics: squared sum test (S2T), sum test (ST), and adaptive test (AT). With less than two values of ρ's, it outputs only p-values for S2T and ST.

Usage

sats(Z, R, W = NULL, rho = c((0:5/10)^2, 0.5, 1))

Arguments

Z	GWAS summary Z-statistics for a set of SNPs
R	SNP pairwise LD matrix
W	SNP weights. Default to equal weights
rho	weights for the ST

Value

p.value

p-values for AT, S2T, and ST

pval

the list of all p-values

rho.est

estimated optimal ρ value

References

Guo,B. and Wu,B.(2018). Statistical methods to detect novel genetic variants using publicly available GWAS summary data. CBC, to appear.

Examples

R = cor(matrix(rnorm(500),100,5)*sqrt(0.8)+rnorm(100)*sqrt(0.2))
Z = rnorm(5) + 0:4
sats(Z,R)

baolinwu/mkatr documentation built on May 14, 2019, 6:03 a.m.