DOQTL (version 1.8.0)

get.pgw: 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.

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)