## HAPLIN, VERSION 4.0 ## Reading data from file... Done There were 5 rows with missing data All rows retained in analysis Preparing data for analysis... Done Running EM for preliminary estimates of haplotype frequencies... Done Removing unused haplotypes... Done Using EM to estimate model with no effect: EM iter: 1 |GLM deviance: 0 |Coefficients: 2.77242e-18 9.39087e-18 2.58269e-18 -6.95332e-19 1.89052e-18 EM iter: 2 |GLM deviance: 345.258 |Coefficients: -0.899013 0.0911016 -1.40653 0.684214 -1.50184 EM iter: 3 |GLM deviance: 344.375 |Coefficients: -0.90182 0.0914246 -1.41264 0.685363 -1.50184 EM iter: 4 |GLM deviance: 344.373 |Coefficients: -0.901826 0.0914253 -1.41265 0.685366 -1.50184 EM iter: 5 |GLM deviance: 344.373 |Coefficients: -0.901826 0.0914253 -1.41265 0.685366 -1.50184 EM iter: 6 |GLM deviance: 344.373 |Coefficients: -0.901826 0.0914253 -1.41265 0.685366 -1.50184 Done Using EM to estimate full model: EM iter: 1 |GLM deviance: 0 |Coefficients: 2.76929e-18 9.29422e-18 2.75979e-18 -4.72029e-19 2.13683e-18 -1.70426e-18 -8.57224e-19 4.06214e-20 -7.75482e-28 1.38221e-17 3.4062e-20 -9.82332e-19 9.32188e-20 9.15247e-20 -8.33508e-19 1.74994e-18 9.11371e-19 1.69407e-21 1.65867e-18 -1.70405e-18 -1.18359e-19 9.62275e-19 1.82625e-18 EM iter: 2 |GLM deviance: 324.308 |Coefficients: -0.786562 0.234966 -1.23777 0.627763 -1.46355 -0.603638 -0.37483 -0.782319 -0.137819 0.942851 -0.262305 0.700751 -0.274264 0.972414 0.30563 0.245949 0.28865 0.00556478 -0.468796 -0.353194 0.717524 0.521617 -14.3119 EM iter: 3 |GLM deviance: 324.026 |Coefficients: -0.785755 0.238644 -1.24484 0.632153 -1.46081 -0.609407 -0.3795 -0.77606 -0.14077 0.953784 -0.258198 0.703041 -0.281416 0.974712 0.301628 0.239555 0.284818 0.00131739 -0.462487 -0.346801 0.728309 0.512107 -14.3091 EM iter: 4 |GLM deviance: 324.025 |Coefficients: -0.785716 0.238678 -1.24486 0.632184 -1.46078 -0.609489 -0.379552 -0.776042 -0.140807 0.953882 -0.258161 0.70306 -0.28148 0.974733 0.301582 0.239504 0.284766 0.00128555 -0.46244 -0.346727 0.728394 0.512041 -14.3091 EM iter: 5 |GLM deviance: 324.025 |Coefficients: -0.785716 0.238678 -1.24486 0.632185 -1.46078 -0.60949 -0.379553 -0.776042 -0.140807 0.953884 -0.258161 0.70306 -0.281481 0.974733 0.301581 0.239504 0.284766 0.0012854 -0.46244 -0.346726 0.728394 0.51204 -14.3091 EM iter: 6 |GLM deviance: 324.025 |Coefficients: -0.785716 0.238678 -1.24486 0.632185 -1.46078 -0.60949 -0.379553 -0.776042 -0.140807 0.953884 -0.258161 0.70306 -0.281481 0.974733 0.301581 0.239504 0.284766 0.0012854 -0.46244 -0.346726 0.728394 0.51204 -14.3091 Done Estimation finished, preparing output... Done Note: Some relative risk estimates fall outside the default plotting range. Consider replotting, with argument "ylim" set wider ################################# ----Arguments supplied to haplin in this run:---- filename: "HAPLIN.trialdata.txt" filespecs: markers = 1:2, n.vars = 0, sep = " ", allele.sep = ";", na.strings = "NA" model: design = "triad", use.missing = TRUE, xchrom = FALSE, maternal = TRUE, test.maternal = FALSE, scoretest = "no" variables: ccvar = NULL, covar = NULL, sex = NULL, comb.sex = "double" haplos: reference = "reciprocal", response = "free", 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: 249 Accounting for possible loss of triads: Cause of loss Triads removed Triads remaining Missing data 0 249 Mendelian incons. 0 249 Unused haplotypes 5 244 Triads remaining for analysis: 244 NOTE: In the following, the most frequent allele is printed as upper-case, all others are lower-case Marker 1: Missing alleles: 6 Allele Frequency Percent 1 149 10.0 2 412 27.7 3 87 5.8 4 840 56.5 total 1488 100.0 Chi-squared test for HWE, p-value: 0.6585 Marker 2: Missing alleles: 4 Allele Frequency Percent C 1397 93.8 t 93 6.2 total 1490 100.0 Chi-squared test for HWE, p-value: 0.5721 -------- Haplotypes removed because of low frequencies: 1-t 2-t 3-t Haplotypes used in the analysis, with coding: 1-C 2-C 3-C 4-C 4-t 1 2 3 4 5 ----Estimation results:---- Date of call: Fri Jan 27 15:01:14 2012 Number of triads: 244 Number of haplotypes: 5 Haplotype frequencies with 95% confidence intervals: Haplotype Frequency(%) lower upper 1-C 11.04 8.03 14.99 2-C 30.62 25.79 35.94 3-C 6.92 4.58 10.42 4-C 45.35 40.08 50.95 4-t 5.59 3.57 8.66 Single- and double dose effects (Relativ Risk) with 95% confidence intervals: Reference method: reciprocal ----Child haplotypes---- Haplotype Dose Relative Risk Lower CI Upper CI P-value 1-C S 0.725 0.46 1.16 0.175 1-C D 1.21 0.386 3.72 0.746 2-C S 1.05 0.706 1.56 0.816 2-C D 0.638 0.309 1.32 0.217 3-C S 0.614 0.341 1.1 0.0966 3-C D 0.686 0.0825 5.55 0.722 4-C S 1.62 1.02 2.56 0.0408 4-C D 1.89 1.05 3.4 0.0354 4-t S 1.26 0.703 2.22 0.44 4-t D 3.59 0.694 17.3 0.13 ----Maternal haplotypes---- Haplotype Dose Relative Risk Lower CI Upper CI P-value 1-C S 1.18 0.732 1.89 0.508 1-C D 0.873 0.188 4.05 0.856 2-C S 1.06 0.713 1.59 0.776 2-C D 0.871 0.439 1.74 0.703 3-C S 1.14 0.652 2.04 0.627 3-C D 2.74 0.552 14.1 0.221 4-C S 0.795 0.531 1.2 0.272 4-C D 1.04 0.618 1.76 0.866 4-t S 0.836 0.464 1.48 0.542 4-t D 2.15e-05 0 Inf 0.991 Overall test for difference between null model (no effects) and full model: ------------ LIKELIHOOD RATIO TEST: Loglike null model: -1228.0728 Loglike full model: -1217.7436 df: 18.0000 Likelihood ratio p-value: 0.2970 (NOTE: The test may be sensitive to rare haplotypes)