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.