get.pgw: Get the genome wide p-value.

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

Get the genome wide p-value.

Description

Given a set of permutations and a LOD or -log10(p-value), return the adjusted genome-wide p-value. This requires autosomal and X chromosome permutation values as provided by scanone.perm. If you are using p-values, make sure to convert both the permutations and the p-values to -log10(-p-value).

Usage

  get.pgw(stat, chr, perms)

Arguments

stat	Numeric vector of mapping statistics. Must be either LOD or -log10(p-values).
chr	Numeric vector of same legnth as stat containing the chromosome on which each statistic occurs.
perms	Numeric matrix with the maximum LOD (or maximum -log10(p-value)) from each permuation.

Value

Numeric vector containing the adjusted genome-wide p-value for each statistic.

Author(s)

Daniel Gatti, Petr Simecek

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.sig.thr

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.