set.threshold: Set the significance threshold

In jendelman/GWASpoly: Genome-wide Association Studies for Autopolyploids

Set the significance threshold

Description

Set the significance threshold

Usage

set.threshold(
  data,
  method = "M.eff",
  level = 0.05,
  n.permute = 1000,
  n.core = 1
)

Arguments

data	Variable of class GWASpoly.fitted
method	One of the following: "M.eff","Bonferroni","FDR","permute"
level	Genome-wide false positive or false discovery rate (depending on method).
n.permute	Number of permutations for method "permute"
n.core	Number of cores to use for multicore processing

Details

The default method, "M.eff", is a Bonferroni-type correction but using an effective number of markers that accounts for LD between markers (Moskvina and Schmidt, 2008). The FDR method is based on version 1.30.0 of the qvalue package.

Value

Variable of class GWASpoly.thresh

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/GWASpoly documentation built on Oct. 16, 2024, 5:59 a.m.