Lmatz: 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 (1) minimum marginal test p-value (minP); SZ test; SZ2 test; and (2) omnibus chi-square test (OT); minimum of OT and SZ2 (MU); and significant at any marginal test.

Usage

Lmatz(Z, Sig, alpha = 5e-08)

Arguments

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

Value

idM

significant SNP list for minP

idSZ

significant SNP list for SZ

idSZ2

significant SNP list for SZ2

idOT

significant SNP list for OT

idMU

significant SNP list for min(SZ2,OT)

idm

SNPs significant at any marginal trait

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.