## HAPLIN, VERSION 4.0 ## Reading data from file... ----- NOTE: You used the (default) value ";" for the "allele.sep" argument. Haplin has assumed you really meant a blank "" instead. ----- Done There were 508 rows with missing data All rows retained in analysis Preparing data for analysis... Done The following 5 data lines were dropped due to Mendelian inconsistencies: 240 257 302 320 780 Running EM for preliminary estimates of haplotype frequencies... Done Removing unused haplotypes... Done Note: The following case/control coding has been assumed: controls = 0, cases = 1 Using EM to estimate model with no effect: EM iter: 1 |GLM deviance: 0 |Coefficients: 1.08862e-18 -6.67302e-19 -1.00047e-20 3.64347e-18 EM iter: 2 |GLM deviance: 359.799 |Coefficients: -0.713055 -1.18646 0.320706 1.27225 EM iter: 3 |GLM deviance: 104.965 |Coefficients: -0.713055 -1.90555 0.224806 1.34845 EM iter: 4 |GLM deviance: 101.348 |Coefficients: -0.713055 -2.02624 0.2036 1.3596 EM iter: 5 |GLM deviance: 101.879 |Coefficients: -0.713055 -2.04019 0.19944 1.36137 EM iter: 6 |GLM deviance: 101.978 |Coefficients: -0.713055 -2.04171 0.198655 1.36167 EM iter: 7 |GLM deviance: 101.994 |Coefficients: -0.713055 -2.04188 0.198509 1.36172 EM iter: 8 |GLM deviance: 101.997 |Coefficients: -0.713055 -2.04189 0.198483 1.36173 EM iter: 9 |GLM deviance: 101.998 |Coefficients: -0.713055 -2.0419 0.198478 1.36173 EM iter: 10 |GLM deviance: 101.998 |Coefficients: -0.713055 -2.0419 0.198477 1.36173 EM iter: 11 |GLM deviance: 101.998 |Coefficients: -0.713055 -2.0419 0.198477 1.36173 EM iter: 12 |GLM deviance: 101.998 |Coefficients: -0.713055 -2.0419 0.198477 1.36173 EM iter: 13 |GLM deviance: 101.998 |Coefficients: -0.713055 -2.0419 0.198477 1.36173 Done Using EM to estimate full model: EM iter: 1 |GLM deviance: 0 |Coefficients: 2.54005e-19 -9.19708e-19 2.24393e-19 3.69194e-18 1.20036e-18 3.1175e-19 EM iter: 2 |GLM deviance: 310.934 |Coefficients: -0.808547 -1.05734 0.26884 1.27994 -1.28603 0.328171 EM iter: 3 |GLM deviance: 89.7213 |Coefficients: -0.893282 -1.79929 0.167796 1.36204 -0.501711 0.387945 EM iter: 4 |GLM deviance: 86.3708 |Coefficients: -0.905895 -1.9526 0.145439 1.37468 -0.342099 0.402278 EM iter: 5 |GLM deviance: 87.1614 |Coefficients: -0.908033 -1.97423 0.140962 1.37675 -0.319404 0.405527 EM iter: 6 |GLM deviance: 87.3163 |Coefficients: -0.908428 -1.97705 0.140093 1.3771 -0.316378 0.40624 EM iter: 7 |GLM deviance: 87.3418 |Coefficients: -0.908505 -1.97742 0.139926 1.37716 -0.315974 0.406393 EM iter: 8 |GLM deviance: 87.346 |Coefficients: -0.90852 -1.97747 0.139895 1.37717 -0.315919 0.406426 EM iter: 9 |GLM deviance: 87.3468 |Coefficients: -0.908524 -1.97747 0.139889 1.37718 -0.315911 0.406432 EM iter: 10 |GLM deviance: 87.3469 |Coefficients: -0.908524 -1.97747 0.139888 1.37718 -0.31591 0.406434 EM iter: 11 |GLM deviance: 87.3469 |Coefficients: -0.908524 -1.97747 0.139888 1.37718 -0.315909 0.406434 EM iter: 12 |GLM deviance: 87.3469 |Coefficients: -0.908524 -1.97747 0.139887 1.37718 -0.315909 0.406434 EM iter: 13 |GLM deviance: 87.3469 |Coefficients: -0.908524 -1.97747 0.139887 1.37718 -0.315909 0.406434 Done Estimation finished, preparing output... Done ################################# ----Arguments supplied to haplin in this run:---- filename: "HAPLIN.trialdata2.txt" filespecs: markers = 1:2, n.vars = 2, sep = " ", allele.sep = "", na.strings = "NA" model: design = "cc.triad", use.missing = TRUE, xchrom = FALSE, maternal = FALSE, test.maternal = FALSE, scoretest = "no" variables: ccvar = 2, covar = NULL, sex = NULL, comb.sex = "double" haplos: reference = "ref.cat", response = "mult", threshold = 0.01, max.haplos = NULL, haplo.file = NULL control: resampling = "no", max.EM.iter = 50, data.out = "no", verbose = TRUE, printout = TRUE ----Data summary:---- Number of triads in original file: 1139 Accounting for possible loss of triads: Cause of loss Triads removed Triads remaining Missing data 0 1139 Mendelian incons. 5 1134 Unused haplotypes 0 1134 Triads remaining for analysis: 1134 NOTE: In the following, the most frequent allele is printed as upper-case, all others are lower-case Marker 1: Missing alleles: 1424 Allele Frequency Percent a 1290 23.8 G 4120 76.2 total 5410 100.0 Chi-squared test for HWE, p-value: 0.6875 Marker 2: Missing alleles: 954 Allele Frequency Percent a 142 2.4 B 5738 97.6 total 5880 100.0 Chi-squared test for HWE, p-value: 0.01014 -------- Haplotypes removed because of low frequencies: a-a Haplotypes used in the analysis, with coding: G-a a-B G-B 1 2 3 ----Estimation results:---- Date of call: Fri Jan 27 15:03:45 2012 Number of triads: 1134 Number of haplotypes: 3 Haplotype frequencies with 95% confidence intervals: Haplotype Frequency(%) lower upper G-a 2.63 2.15 3.26 a-B 21.88 20.44 23.42 G-B 75.47 73.87 76.94 Single- and double dose effects (Relativ Risk) with 95% confidence intervals: Reference method: ref.cat Reference category: 3 ----Child haplotypes---- Haplotype Dose Relative Risk Lower CI Upper CI P-value G-a S 0.729 0.402 1.31 0.285 G-a D 0.532 0.162 1.7 0.285 a-B S 1.5 1.23 1.82 0 a-B D 2.24 1.52 3.33 0 G-B S 1 1 1 1 G-B D 1 1 1 1 Overall test for difference between null model (no effects) and full model: ------------ LIKELIHOOD RATIO TEST: Loglike null model: -3117.5699752 Loglike full model: -3108.4934459 df: 2.0000000 Likelihood ratio p-value: 0.0001143 (NOTE: The test may be sensitive to rare haplotypes)