Adjusted P values for genome-wide scans.
Genome-wide scans for quantitative trait loci (QTL) have traditionally been summarized with plots of logarithm of odds (LOD) scores. A valuable modification is to supplement such plots with an additional vertical axis displaying quantiles of adjusted P values and labeling local maxima of the LOD scores with location-specific adjusted P values. This provides a visible gradation of genome-wide significance for the LOD score curve, instead of the stark dichotomy that a single threshold yields. Adjusted P values give genome-wide significance of individual LOD scores and are obtained through a straightforward modification of the familiar algorithm for generating permutation-based thresholds.
Lystig
Theodore C
TC
Department of Mathematical Statistics, Chalmers University of Technology, Eklandagatan 86, 412 96 Göteborg, Sweden. lystig@math.chalmers.se
D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics; D003198:Computer Simulation; D003433:Crosses, Genetic; D004843:Epistasis, Genetic; D005819:Genetic Markers; D014644:Genetic Variation; D016678:Genome; D008126:Lod Score; D011336:Probability; D019655:Quantitative Trait, Heritable; D051381:Rats
D005819:Genetic Markers