get.pgw {DOQTL} | R Documentation |
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).
get.pgw(stat, chr, perms)
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. |
Numeric vector containing the adjusted genome-wide p-value for each statistic.
Daniel Gatti, Petr Simecek
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.
## Not run: perms = scanone.perm(pheno = pheno, probs = probs, addcovar = addcovar, snps = anps) get.sig.thr(perms) ## End(Not run)