MultiSecondary: Conditional multivariate association analysis using summary...

In MultiABEL: Multi-Trait Genome-Wide Association Analysis

Description

This function is developed to implement cMVA based on multivariate results

Usage

MultiSecondary(gwa.region, LD.ref, snp.ref, R.ref, p.threshold = 5e-08,
  tol = 0.8, traits, v_y = NULL, T2.return = FALSE)

Arguments

gwa.region	GWAS summary statistics, includes A1, A2 and three columns for each trait: beta, se and N
LD.ref	Regional LD matrix including SNPs in gwa.region
snp.ref	The reference alleles of SNPs in the reference LD correlation matrix. The names of the vector should be SNP names in reference sample
R.ref	Shrinkage phenotypic correlation matrix, achieved from load.summary()
p.threshold	P-value threshold in conditional analysis
tol	Tolerance for multicollinearity
traits	Traits to be analyzed
v_y	The variance of the traits
T2.return	Returning conditional T2 statistic or not

Value

The function returns a list with elements of T2.sele: The conditional test statistic of the selected variants. It will be provided if T2.return = TRUE; p.sele: The conditional p-value of the selected variants; b_joint.sele: The conditional effect size of the selected variants; se_b_joint.sele: The conditional standard error of the selected variants.

Author(s)

Zheng Ning, Xia Shen

References

Zheng Ning, Yakov Tsepilov, Sodbo Zh. Sharapov, Alexander K. Grishenko, Masoud Shirali, Peter K. Joshi, James F. Wilson, Yudi Pawitan, Chris S. Haley, Yurii S. Aulchenko, Xia Shen (2018). Multivariate discovery, replication, and interpretation of pleiotropic loci using summary association statistics. Submitted.

See Also

MultiSummary

Examples

## Not run: 
data(example.MultiSecondary)
##### 474 snps around rs905938 #####

## Six-traits cMVA ##
traits <- c("HEIGHT", "BMI", "HIP", "WC", "WHR", "WEIGHT")
MultiSecondary(gwa.region = example.gwas, LD.ref = example.LD, 
				  snp.ref = example.snp.ref, R.ref = example.R.ref,
               p.threshold = 5e-8, tol = 0.9, traits = traits, T2.return = TRUE)

## Three-traits cMVA ##
traits <- c("HEIGHT", "BMI", "HIP")
MultiSecondary(gwa.region = example.gwas, LD.ref = example.LD, 
               snp.ref = example.snp.ref, R.ref = example.R.ref,
               p.threshold = 5e-4, tol = 0.9, traits = traits, T2.return = TRUE)

## End(Not run)

MultiABEL documentation built on May 2, 2019, 5:57 p.m.