corMeta.fixef: The fixed effects meta-analysis estimator accounting for...

In tamartsi/MetaCor: Performs Stratified SNP-trait analysis and combines the results using the MetaCor method

Description

Computes the fixed effects meta-analysis estimator while accounting for correlations between effect estimates in the variance estimation. The computation is done for many SNPs at once.

Usage

corMeta.fixef(beta, var, cov)

Arguments

beta	a p by S matrix of estimated effects of each of p SNPs on a trait in each of S strata.
var	a p by S matrix of variances of the estimated effects of each of p SNPs on a trait in each of S strata.
cov	a p by (S*(S-1)/2) matrix representing p vectors of covariances between the estimated effects of each of p SNPs on a trait in each of S strata.

Details

This function requires column names for each of the columns. It is used by stratLMMTest, which prepares the data with correct column names.

Value

a matrix with beta, var, test.stat and pval corresponding to the meta-analysis estimates for each of the SNPs, their variances, the test statistics and their p-values.

Note

This function is called by MetaCor and it is advisable to use MetaCor. It can also be called directly, but then the test of heterogeneity is not performed. Also, MetaCor allows for selection of strata while this function does not.

Author(s)

Tamar Sofer

Examples

### create a small data set with the right formating:
require(mvtnorm)
n.strat <- 5
n.est <- 5
## create a positive definite matrix to be a covariance matrix
sigma <- matrix(rnorm(n.strat^2), n.strat, n.strat)
sigma <- t(sigma) 

effects <- rmvnorm(n.est, c(2,2,3,3,0), sigma)
colnames(effects) <- paste0("Beta.s", 1:n.strat)
vars <- matrix(rep(diag(sigma), n.est), nrow = n.est, ncol = n.strat, byrow = T)
colnames(vars) <- paste0("var.s", 1:n.strat)
covs <- matrix(rep(sigma[lower.tri(sigma)], n.est), nrow = n.est, byrow = T)
colnames(covs) <- c(paste0("cov.s1:", paste0("s", 2:n.strat)), paste0("cov.s2:", paste0("s", 3:n.strat)), paste0("cov.s3:", paste0("s", 4:n.strat)) , "cov.s4:s5")

## test:
corMeta.fixef(effects, vars, covs) 

tamartsi/MetaCor documentation built on May 31, 2019, 2:56 a.m.