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Accounting for Variability in the Use of Permutation Testing to Detect Quantitative Trait Loci
Author(s) -
Nettleton Dan,
Doerge R. W.
Publication year - 2000
Publication title -
biometrics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.298
H-Index - 130
eISSN - 1541-0420
pISSN - 0006-341X
DOI - 10.1111/j.0006-341x.2000.00052.x
Subject(s) - permutation (music) , test statistic , quantitative trait locus , trait , statistical hypothesis testing , statistic , multiple comparisons problem , resampling , confidence interval , sample size determination , monte carlo method , asymptotic distribution , statistics , computer science , biology , genetics , mathematics , gene , physics , estimator , acoustics , programming language
Summary. Locating quantitative trait loci (QTL), or genomic regions associated with known molecular markers, is of increasing interest in a wide variety of applications ranging from human genetics to agricultural genetics. The hope of locating QTL (or genes) affecting a quantitative trait is that it will lead to characterization and possible manipulations of these genes. However, the complexity of both statistical and genetic issues surrounding the location of these regions calls into question the asymptotic statistical results supplying the distribution of the test statistics employed. Coupled with the power of current‐day computing, permutation theory was reintroduced for the purpose of estimating the distribution of any test statistic used to test for the location of QTL. Permutation techniques have offered an attractive alternative to significance measures based on asymptotic theory. The ideas of permutation testing are extended in this application to include confidence intervals for the thresholds and p ‐values estimated in permutation testing procedures. The confidence intervals developed account for the Monte Carlo error associated with practical applications of permutation testing and lead to an effective method of determining an efficient permutation sample size.