get.gev.thresholds: Returns a significance threshold based on fitting max LODs or...

In gkeele/miqtl: Suite of QTL Mapping Functions

Returns a significance threshold based on fitting max LODs or max -log10p to a generalized extreme value (GEV) distribution

Description

This function takes an scan.h2lmm() object, and returns a specified number of outcome samples, either permutations or from the null model of no locus effect.

Usage

get.gev.thresholds(
  threshold.scans,
  use.lod = FALSE,
  percentile = 0.95,
  type = c("min", "max")
)

Arguments

threshold.scans	Output object from run.threshold.scans().
use.lod	DEFAULT: FALSE. "TRUE" specifies LOD scores. "FALSE" specifies p-values.
percentile	DEFAULT: 0.95. The desired alpha level (false positive probability) from the GEV distribution.
type	DEFAULT: "min". If "min", the minimum statistics are expected, which is usually desired with p-values - though they are transformed to maxima using -log10(). If "max", the maximum statistics are expected. This is mainly expected to be used with mediation scans for direct mediations (p-value drop).

Examples

get.gev.thresholds()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.