Open AccessAdjusted P Values for Genome-Wide Scans
Author(s) -
Theodore C. Lystig
Publication year - 2003
Publication title -
genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.792
H-Index - 246
eISSN - 1943-2631
pISSN - 0016-6731
DOI - 10.1093/genetics/164.4.1683
Subject(s) - genome , quantile , permutation (music) , quantitative trait locus , biology , logarithm , genetics , maxima , trait , statistics , computational biology , mathematics , gene , computer science , physics , mathematical analysis , performance art , acoustics , programming language , art history , art
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.