get.sig.thr: Get the significance thresholds.

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

Get the significance thresholds.

Description

Given a set of permutations, return the significance thresholds on the autosomes and X chromosome.

Usage

  get.sig.thr(perms, alpha = 0.05, Xchr = TRUE)

Arguments

perms	Numeric matrix with the maximum LOD (or maximum -log10(p-value)) from each permuation.
alpha	Numeric vector containing the alpha level of the significance thresholds.
Xchr	Logical value (default = TRUE) that indicates that the permutations contain both autosomal and X chromosome thresholds.

Value

Numeric matrix containing the significance thresholds for the autosomes in column 1 an dthe X chromossome in column 2.

Author(s)

Daniel Gatti

References

The X chromosome in quantitative trait locus mapping. Broman KW, Sen S, Owens SE, Manichaikul A, Southard-Smith EM, Churchill GA. Genetics. 2006 Dec;174(4):2151-8.

See Also

get.pgw

Examples

  ## Not run:  
    perms = scanone.perm(pheno = pheno, probs = probs, addcovar = addcovar, snps = anps)
    get.sig.thr(perms) 
  
## End(Not run)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.