Lemats: Compute the list of significant SNPs using the GWAS summary...

In baolinwu/MTAR: Various Multi-Trait Association tests in R

Description

We compute the significant SNPs for three tests: omnibus chi-square test (OT); 1-DF PC test (ET); adaptive test (AT).

Usage

Lemats(Z, Sig, rho = 0:5/5, alpha = 5e-08)

Arguments

Z	matrix of summary Z-statistics (SNPs by traits)
Sig	the estimated marginal trait correlation matrix
rho	sequence of weights assigned to the 1-DF test
alpha	desired genome-wide significance level (default to 5E-8)

Value

idQ

significant SNP list for OT

idE

significant SNP list for ET

idA

significant SNP list for AT

References

Guo,B. and Wu,B. (2018) Integrate multiple traits to detect novel disease-gene association using GWAS summary data with an adaptive test approach. Bioinformatics, under revision.

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