eff_nbr_tests: Effective number of tests

In sinarueeger/GWAS.utils: Helper functions for GWAS data

Description

Calculates the effective number of tests performed in a GWAS, given the LD structure among the SNPs. SNPs that are highly correlated are not counted twice.

Usage

eff_nbr_tests(mat, cor.true = FALSE)

Arguments

mat	matrix, either individual by SNPs (n x p) matrix, or correlation matrix between SNPs
cor.true	indicates if option mat is a correlation matrix or not

Value

zhc.correction number of effective tests

References

Implemented from https://www.ncbi.nlm.nih.gov/pubmed/18271029

Examples

dat.sim <- data.frame(g = rnorm(100)) %>% dplyr::mutate(g2 = g * 2)
eff_nbr_tests(diag(10), cor.true = TRUE) ## 10, because all are independent
eff_nbr_tests(dat.sim, cor.true = FALSE)

sinarueeger/GWAS.utils documentation built on July 30, 2019, 5:21 p.m.