PheSATS: GWAS summary data based phenome-wide SNP-set association test

In baolinwu/MSKAT: Various multi-trait variant-set association test methods

Description

Efficient and powerful summary data based phenome-wide SNP-set association tests: quadratic test (S2T), burden test (SBT), their adaptive test: Fisher combination test (FCT), and Tippett combination test (TCT).

Usage

PheSATS(Z, Sig, R)

Arguments

Z	M by K matrix of summary Z-statistics for M variants across K traits
Sig	estimated trait correlation matrix (K by K)
R	variant LD correlation matrix (M by M)

Value

p-value vector: FCT, SBT, S2T, TCT, and S2E (residual effects excluding SBT)

References

Guo,B., Bishop,J., Liu,N. and Wu,B. (2018) Phenome-wide SNP-set association test based on GWAS summary data to identify novel disease-gene association. tech rep.

Examples

K = 4; M = 20
R = cor(matrix(rnorm(500*M),500,M)*sqrt(0.8)+rnorm(500)*sqrt(0.2))
Y = matrix(rnorm(100*K), 100,K)*sqrt(0.8)+rnorm(100)*sqrt(0.2); Y[,1] = -Y[,1]
Sig = cor(Y)
Rc = t(chol(R)); Sc = chol(Sig)
Z0 = Rc%*%matrix(rnorm(K*M),M,K)%*%Sc
PheSATS(Z0,Sig,R)
js = sample(1:M, size=round(M*0.4))
Z1 = Z0; Z1[js,] = Z1[js,] + 1.5
PheSATS(Z1,Sig,R)
ij = cbind(sample(1:M, size=20, rep=TRUE), sample(1:K, size=20, rep=TRUE))
Z2 = Z0; Z2[ij] = Z2[ij] + rnorm(20)*1.5
PheSATS(Z2,Sig,R)

baolinwu/MSKAT documentation built on May 28, 2019, 6:37 p.m.