WARNING - Command line parameter -snip (#10) ignored QTDT - Quantitative TDT 2.2.1 (c) 1998-2001 Goncalo Abecasis (goncalo@well.ox.ac.uk) This program implements tests described by Abecasis et al, Am J Hum Genet 66:279-292 (2000) Abecasis et al, Eur J Hum Genet 8:545-551 (2000) and others The following parameters are in effect: QTDT Data File : keavney.dat (-dname) QTDT Pedigree File : keavney.ped (-pname) QTDT IBD Status File : merlin.ibd (-iname) Missing Value Code : -99.999 (-xname) Covariates : USER SPECIFIED (-c{p|s|u|-|}) Association Model : ORTHOGONAL (-a[a|d|f|m|o|p|r|t|w|-]) Full Model Variances : NON SHARED (-v{e|c|g|n|t|a|d|-|}) & POLYGENIC & ADDITIVE Null Model Variances : NON SHARED (-w{e|c|g|n|t|a|d|-|}) & POLYGENIC Parent of Origin Effects : NONE (-o[f|t|m|p|-]) Monte-Carlo Permutations : 0 (-m9999) Numeric Minimizer : NELDER AND MEAD (-n[n|p]) Transmission Scoring : FULL PEDIGREE (-t[n|p]) Additional Options --dominance, --snp, --multi-allelic, --references, --exclude-founder-phenotypes Online documentation http://www.well.ox.ac.uk/asthma/QTDT Comments, bugs: goncalo@well.ox.ac.uk The following models will be evaluated... NULL MODEL Means = Mu + B + W Variances = Ve + Vg FULL MODEL Means = Mu + B + W Variances = Ve + Vg + Va Testing trait: Angiotensin ============================================= Testing marker: t-5491c --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 387 481.65 386 476.81 9.69 0.0019 ( 186/392 probands) 2 : 387 481.65 386 476.81 9.69 0.0019 ( 186/392 probands) Testing marker: a-5466c --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 385 480.29 384 476.57 7.44 0.0064 ( 190/390 probands) 2 : 385 480.29 384 476.57 7.44 0.0064 ( 190/390 probands) Testing marker: t-3892c --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 392 478.96 391 476.20 5.53 0.0187 ( 214/397 probands) 2 : 392 478.96 391 476.20 5.53 0.0187 ( 214/397 probands) Testing marker: a-240t --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 393 491.36 392 487.95 6.81 0.0090 ( 196/398 probands) 2 : 393 491.36 392 487.95 6.81 0.0090 ( 196/398 probands) Testing marker: t-93c --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 384 481.36 383 477.77 7.19 0.0073 ( 188/389 probands) 2 : 384 481.36 383 477.77 7.19 0.0073 ( 188/389 probands) Testing marker: t-1237c --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 369 448.68 368 446.30 4.78 0.0288 ( 199/374 probands) 2 : 369 448.68 368 446.30 4.78 0.0288 ( 199/374 probands) Testing marker: g2215a --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 364 424.66 363 424.37 0.59 ( 200/369 probands) 2 : 364 424.66 363 424.37 0.59 ( 200/369 probands) Testing marker: i/d --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 393 457.77 392 457.65 0.24 ( 216/398 probands) 2 : 393 457.77 392 457.65 0.24 ( 216/398 probands) Testing marker: g2350a --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 360 418.64 359 418.62 0.04 ( 187/365 probands) 2 : 360 418.64 359 418.62 0.04 ( 187/365 probands) Testing marker: 4656ct --------------------------------------------- Allele df(0) LnLk(0) df(V) LnLk(V) ChiSq p 1 : 382 442.26 381 441.21 2.09 ( 215/387 probands) 2 : 382 442.26 381 441.21 2.09 ( 215/387 probands)