gwas_threshold: Compute GWAS discovery threshold

In jendelman/StageWise: Two-stage analysis of multi-environment trials for genomic selection and GWAS

Compute GWAS discovery threshold

Description

Compute GWAS discovery threshold

Usage

gwas_threshold(geno, alpha = 0.05, exclude.chrom = NULL, n.core = 1)

Arguments

geno	object of class_geno
alpha	genome-wide significance level
exclude.chrom	chromosomes to exclude
n.core	number of cores to use

Details

Uses a Bonferroni-type correction based on an effective number of markers that accounts for LD (Moskvina and Schmidt, 2008).

Value

-log10(p) threshold

References

Moskvina V, Schmidt KM (2008) On multiple-testing correction in genome-wide association studies. Genetic Epidemiology 32:567-573. doi:10.1002/gepi.20331

jendelman/StageWise documentation built on Feb. 23, 2025, 11 a.m.