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Table 1 Four models compared in the three likelihood-ratio tests

From: Identifying single-nucleotide polymorphisms responsible for the linkage signal of rheumatoid arthritis on chromosome 6 by joint modeling of linkage and association

Modela   Likelihood d.f. Parametersb LR tests
(1) BM L(θ = 1 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabigdaXaqaaiabikdaYaaaaaa@2E9E@ , r2 = 0) 1 p A  
(2) LE L(θ = 0, r2= 0) 4 p A , p D , f DD , f Dd , f dd (2) vs. (1): test for linkage
(3) GM L(θ = 0, 0 <r2 < 1) 5 p DA , p Da , P dA , f DD , f Dd , f dd (3) vs. (2): test for association in the presence of linkage
(4) LD L(θ = 0, r2 = 1) 3 p A , f DD , f Dd , f dd (3) vs. (4): test for other linked variants
  1. aBM, base model; LE, linkage equilibrium; GM, general model; LD, linkage disequilibrium.
  2. bP A = marker allele frequency; P D = disease allele frequency; f g = P(affected | g), g {DD, Dd, dd}; p DA , p Da , p dA are the marker-disease haplotype frequencies.