README.md

In Vivian-Liu-Wei64/Omni_Multi: Omnibus Test for Detecting Multiple Phenotye Association

omniTest：An Omnibus Test for Detecting Multiple Phenotype Associations based on GWAS Summary Level Data

omniTest includs three approches (GHC, GBJ and OMNI) for detecting the association between a single SNP and multiple traits based on GWAS summary statistics while accounting for the correlation structure among multiple traits.

Setup

Please use the following command in R to install the package:

install.packages("devtools") 
library(devtools)
install_github("Vivian-Liu-Wei64/Omni_Multi")

Usage

The omniTest performs the multiple traits association test based on GWAS summary statistics.

The Multi_Analysis function is used to calculate the P_values of GHC, GBJ, MinP and OMNI tests.

Multi_Analysis(Z_score, Sigma)

Given Z_score and Sigma, the Multi_Analysis function provids the P-values of the GHC, GBJ and OMNI tests.

Example

library(omniTest)  # load the omniTest package

# Z_score shold be a vector of test statistics for each factor in the set (i.e. marginal test statistic for each trait).

# Sigma shpuld be a matrix of the correlations between all the test statistics in the set.

#example 

Sigma<-matrix(rep(1,9),3,3)  

diag(Sigma)<-rep(1,3)

Z_score<- rmvnorm(1,mean=c(2,2,2),sigma=Sigma) 

Multi_Analysis(Z_score,Sigma) 


-----------The p_values of GHC, GBJ, MinP and OMNI tests-----------

      GHC_p      GBJ_p    MinP_p    OMNI_p
[1] 0.9103539 1.0000000 0.9971193 1.0000000

Reference

Liu, W., Guo, Y. and Liu, Z.#, 2021. An Omnibus Test for Detecting Multiple Phenotype Associations based on GWAS Summary Level Data. (in press)

Vivian-Liu-Wei64/Omni_Multi documentation built on Dec. 18, 2021, 6:20 p.m.