From 0bdeca3490c1ddbb7fa29165893a97f90eeefba7 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Fri, 6 Jun 2014 22:00:30 +0000 Subject: Implimented Karl Broman's lodchart code for the interval mapping function. Suggestive/significant bars and additive effect curve added --- web/gemma/BXD.fam | 93 + web/gemma/HLC.fam | 744 +- web/gemma/output/HLC_output.assoc.txt | 546698 +++++++++++++++---------------- web/gemma/output/HLC_output.log.txt | 24 +- 4 files changed, 273826 insertions(+), 273733 deletions(-) create mode 100644 web/gemma/BXD.fam (limited to 'web/gemma') diff --git a/web/gemma/BXD.fam b/web/gemma/BXD.fam new file mode 100644 index 00000000..e4906c38 --- /dev/null +++ b/web/gemma/BXD.fam @@ -0,0 +1,93 @@ +BXD1 BXD1 0 0 0 x +BXD2 BXD2 0 0 0 x +BXD5 BXD5 0 0 0 0.333 +BXD6 BXD6 0 0 0 x +BXD8 BXD8 0 0 0 x +BXD9 BXD9 0 0 0 x +BXD11 BXD11 0 0 0 x +BXD12 BXD12 0 0 0 x +BXD13 BXD13 0 0 0 x +BXD14 BXD14 0 0 0 1.000 +BXD15 BXD15 0 0 0 x +BXD16 BXD16 0 0 0 x +BXD18 BXD18 0 0 0 x +BXD19 BXD19 0 0 0 x +BXD20 BXD20 0 0 0 x +BXD21 BXD21 0 0 0 0.500 +BXD22 BXD22 0 0 0 x +BXD23 BXD23 0 0 0 x +BXD24a BXD24a 0 0 0 x +BXD24 BXD24 0 0 0 x +BXD25 BXD25 0 0 0 x +BXD27 BXD27 0 0 0 x +BXD28 BXD28 0 0 0 x 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--git a/web/gemma/output/HLC_output.assoc.txt b/web/gemma/output/HLC_output.assoc.txt index d10b9137..2590adca 100644 --- a/web/gemma/output/HLC_output.assoc.txt +++ b/web/gemma/output/HLC_output.assoc.txt @@ -1,273350 +1,273350 @@ chr rs ps n_miss allele1 allele0 af beta se l_remle p_wald -0 rs1155740 0 18 T C 0.274 -2.240216e+02 4.164460e+02 1.523933e+00 5.909023e-01 -0 rs1169469 0 16 T C 0.105 2.174367e+02 5.970349e+02 1.419431e+00 7.158941e-01 -0 rs11775 0 19 G A 0.327 -5.104841e+02 3.949663e+02 1.471936e+00 1.968950e-01 -0 rs1368258 0 13 T C 0.343 2.385588e+02 4.059932e+02 1.526747e+00 5.571175e-01 -0 rs1414747 0 17 A C 0.446 1.852007e+02 3.610211e+02 1.425848e+00 6.082239e-01 -0 rs1459037 0 7 G A 0.290 -1.804489e+02 4.075582e+02 1.269764e+00 6.581674e-01 -0 rs150775 0 20 T G 0.061 -5.712922e+02 7.776945e+02 1.549698e+00 4.629900e-01 -0 rs1538704 0 6 G A 0.292 -2.612568e+01 3.846693e+02 1.386052e+00 9.458834e-01 -0 rs1578301 0 0 C T 0.447 6.069556e+01 3.729657e+02 1.413331e+00 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3.334989e-01 -1 rs4040617 819184 0 G A 0.129 -5.045850e+02 5.380922e+02 1.628821e+00 3.489159e-01 -1 rs4075116 1043551 3 G A 0.303 -3.267727e+02 3.829465e+02 1.493635e+00 3.939672e-01 -1 rs10907175 1170649 2 C A 0.104 -5.656413e+02 5.879317e+02 1.291888e+00 3.365531e-01 -1 rs6603781 1198553 9 A G 0.104 6.873717e+01 6.357358e+02 1.425143e+00 9.139498e-01 -1 rs6685064 1251214 1 T C 0.072 -2.027760e+01 6.823540e+02 1.493638e+00 9.763066e-01 -1 rs1695824 1450836 7 G T 0.242 5.862496e+02 4.232862e+02 8.607368e-01 1.667804e-01 -1 rs3766180 1563419 10 G A 0.294 -1.309884e+02 3.841362e+02 1.472114e+00 7.332762e-01 -1 rs6603791 1586207 5 G A 0.315 -5.761242e+01 3.818433e+02 1.444871e+00 8.801422e-01 -1 rs2281173 1720353 8 A G 0.094 2.843505e+02 6.094251e+02 1.422139e+00 6.410337e-01 -1 rs1107910 1724482 11 G A 0.444 -5.433594e+02 3.597552e+02 1.438618e+00 1.316949e-01 -1 rs2272908 1753640 6 T C 0.499 2.338570e+02 3.407275e+02 1.424214e+00 4.928690e-01 -1 rs3737628 1755093 7 T C 0.496 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151873256 3 A G 0.065 1.890174e+01 7.121391e+01 1.853814e+01 7.908131e-01 +23 rs6627738 151900925 14 C T 0.059 1.303397e+00 7.498440e+01 1.847675e+01 9.861398e-01 +23 rs4828744 151925407 4 G A 0.070 -3.798626e+01 6.895173e+01 1.844461e+01 5.819842e-01 +23 rs4828747 151929154 8 C T 0.074 -3.017982e+01 6.811388e+01 1.842847e+01 6.579341e-01 +23 rs2008144 151966996 4 A G 0.069 -2.943911e+01 6.996560e+01 1.844574e+01 6.741390e-01 +23 rs5925336 151987489 20 T C 0.189 1.609660e+01 4.633787e+01 1.843431e+01 7.284819e-01 +23 rs1894342 151987996 11 G A 0.066 -2.553947e+01 7.205729e+01 1.845115e+01 7.231903e-01 +23 rs1557505 151992064 2 G A 0.181 8.774293e+00 4.599956e+01 1.845407e+01 8.488146e-01 +23 rs5924813 151995603 7 C T 0.060 -1.248185e+01 7.535556e+01 1.848287e+01 8.685195e-01 +23 rs2012435 152010745 2 T C 0.068 -3.299124e+01 7.021400e+01 1.844778e+01 6.386910e-01 +23 rs2012436 152010777 2 G C 0.068 -3.299124e+01 7.021400e+01 1.844778e+01 6.386910e-01 +23 rs5925368 152033116 13 G A 0.056 -2.343574e+01 7.986446e+01 1.843571e+01 7.693261e-01 +23 rs6627772 152053967 5 A G 0.327 -6.007694e+01 3.732501e+01 1.822900e+01 1.082358e-01 +23 rs995423 152085362 13 A T 0.488 7.303934e+00 3.601547e+01 1.851164e+01 8.393885e-01 +23 rs1894354 152089815 0 T C 0.177 6.630538e+01 4.741609e+01 1.884928e+01 1.627303e-01 +23 rs5986911 152351829 6 T A 0.036 -1.035313e+02 1.018708e+02 1.852546e+01 3.100646e-01 +23 rs5945145 152351894 5 C T 0.405 -6.771207e+01 3.625774e+01 1.825853e+01 6.251707e-02 +23 rs4898424 152360329 16 G T 0.274 8.033843e+00 4.078294e+01 1.850072e+01 8.439293e-01 +23 rs4898428 152397543 12 A G 0.134 -7.439240e+01 5.408980e+01 1.851850e+01 1.697474e-01 +23 rs3761536 152427138 16 A T 0.178 -9.077789e+00 4.773908e+01 1.842684e+01 8.492790e-01 +23 rs5987140 152521101 20 C T 0.111 -8.139822e+01 6.008733e+01 1.883675e+01 1.762439e-01 +23 rs2266887 152760433 8 T G 0.203 1.642004e+01 4.559164e+01 1.851033e+01 7.189104e-01 +23 rs7884370 152843727 5 G A 0.041 1.067922e+02 8.846300e+01 1.840011e+01 2.280280e-01 +23 rs1734791 152851766 13 T A 0.158 9.587664e+00 4.967442e+01 1.820023e+01 8.470433e-01 +23 rs766420 153075250 6 C G 0.220 -1.529738e+00 4.346124e+01 1.847741e+01 9.719386e-01 +23 rs766419 153075507 6 C T 0.219 5.737501e-01 4.345172e+01 1.847069e+01 9.894710e-01 +23 rs2239467 153076140 14 G A 0.224 -3.840245e+00 4.359747e+01 1.848352e+01 9.298513e-01 +23 rs4898494 153174968 5 T A 0.108 1.026851e+02 5.741392e+01 1.815588e+01 7.440664e-02 +23 rs4898348 153450097 18 T C 0.231 3.028263e+01 4.381115e+01 1.867799e+01 4.898121e-01 +23 rs5945109 153471452 8 G A 0.377 4.265276e+01 3.755346e+01 1.870105e+01 2.566856e-01 +23 rs5945122 153737610 8 C A 0.135 -1.257540e-01 5.316144e+01 1.847772e+01 9.981137e-01 +23 rs2051161 153849554 3 G C 0.383 5.518998e+01 3.716065e+01 1.853114e+01 1.382394e-01 +23 3885427 154017791 18 G A 0.232 -2.497275e+01 4.205623e+01 1.870675e+01 5.529657e-01 +23 rs475025 154048640 3 G A 0.243 -9.176948e+00 4.103539e+01 1.841459e+01 8.231488e-01 +23 rs6420603 154316683 14 G A 0.029 2.034603e+02 1.089822e+02 1.854842e+01 6.260192e-02 +23 rs574386 154411192 9 C T 0.240 -3.082872e+00 4.080390e+01 1.831726e+01 9.398100e-01 diff --git a/web/gemma/output/HLC_output.log.txt b/web/gemma/output/HLC_output.log.txt index e8107112..f7c9f5d2 100644 --- a/web/gemma/output/HLC_output.log.txt +++ b/web/gemma/output/HLC_output.log.txt @@ -10,19 +10,19 @@ ## number of phenotypes = 1 ## number of total SNPs = 358499 ## number of analyzed SNPs = 273349 -## REMLE log-likelihood in the null model = -4252.51 -## MLE log-likelihood in the null model = -4261.76 -## pve estimate in the null model = 0.314624 -## se(pve) in the null model = 0.403683 -## vg estimate in the null model = 2.61389e+07 -## ve estimate in the null model = 1.88332e+07 -## beta estimate in the null model = 5107.48 -## se(beta) = 210.014 +## REMLE log-likelihood in the null model = -3351.61 +## MLE log-likelihood in the null model = -3357.96 +## pve estimate in the null model = 0.858988 +## se(pve) in the null model = 0.0889649 +## vg estimate in the null model = 1.0633e+06 +## ve estimate in the null model = 57733.1 +## beta estimate in the null model = 620.978 +## se(beta) = 11.6278 ## ## Computation Time: -## total computation time = 2.5965 min +## total computation time = 2.67033 min ## computation time break down: -## time on eigen-decomposition = 0.0015 min -## time on calculating UtX = 0.414167 min -## time on optimization = 2.03267 min +## time on eigen-decomposition = 0.00183333 min +## time on calculating UtX = 0.399833 min +## time on optimization = 2.12417 min ## -- cgit v1.2.3