From 515662ecabd5d3a90eef6987aa5f8d4dbe63611f Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Mon, 19 May 2014 22:03:31 +0000 Subject: Fixed sorting on the show trait page Added/improved the x and y axis on the bar graph and histogram GEMMA working but still really slow --- web/gemma/output/HLC_output.assoc.txt | 546698 +++++++++++++++---------------- web/gemma/output/HLC_output.log.txt | 22 +- 2 files changed, 273360 insertions(+), 273360 deletions(-) (limited to 'web') diff --git a/web/gemma/output/HLC_output.assoc.txt b/web/gemma/output/HLC_output.assoc.txt index 066b2e6d..d10b9137 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 3.657362e+01 2.959468e+01 1.474382e+01 2.172090e-01 -0 rs1169469 0 16 T C 0.105 1.051056e+01 4.306356e+01 1.484068e+01 8.072938e-01 -0 rs11775 0 19 G A 0.327 -3.713332e+01 2.802305e+01 1.327030e+01 1.858502e-01 -0 rs1368258 0 13 T C 0.343 4.317085e+01 2.884774e+01 1.515606e+01 1.352637e-01 -0 rs1414747 0 17 A C 0.446 7.444262e+00 2.577342e+01 1.474551e+01 7.728486e-01 -0 rs1459037 0 7 G A 0.290 -8.095321e+00 2.877323e+01 1.467617e+01 7.785796e-01 -0 rs150775 0 20 T G 0.061 -4.064932e+00 5.527824e+01 1.486203e+01 9.414143e-01 -0 rs1538704 0 6 G A 0.292 -1.015838e+01 2.739498e+01 1.471320e+01 7.109626e-01 -0 rs1578301 0 0 C T 0.447 1.596911e+01 2.657632e+01 1.482601e+01 5.482419e-01 -0 rs16907085 0 1 G A 0.124 4.403192e+01 4.017091e+01 1.468063e+01 2.736494e-01 -0 rs16992891 0 3 T C 0.333 9.826730e-02 2.708139e+01 1.483524e+01 9.971065e-01 -0 rs17566573 0 20 A G 0.195 3.087860e+01 3.361346e+01 1.478049e+01 3.588060e-01 -0 rs2229935 0 1 T C 0.275 -2.691205e+01 2.919483e+01 1.498852e+01 3.571513e-01 -0 rs2230394 0 5 T C 0.098 1.171663e+01 4.486701e+01 1.489657e+01 7.941100e-01 -0 rs2230395 0 1 C A 0.101 2.252935e+01 4.418118e+01 1.493292e+01 6.103646e-01 -0 rs2387949 0 8 A G 0.119 1.815905e+01 3.850873e+01 1.478549e+01 6.374853e-01 -0 rs2565615 0 21 T A 0.498 -1.543149e+00 2.721993e+01 1.480421e+01 9.548173e-01 -0 rs2886026 0 5 G A 0.435 -1.149330e+01 2.657613e+01 1.492739e+01 6.656212e-01 -0 rs2886027 0 18 A G 0.436 -4.772916e+00 2.702424e+01 1.487982e+01 8.598941e-01 -0 rs2903177 0 11 G A 0.050 -3.740485e+01 5.665480e+01 1.380411e+01 5.094678e-01 -0 rs2903407 0 1 G A 0.130 8.295727e+01 3.856454e+01 1.454574e+01 3.202913e-02 -0 rs3818890 0 7 A G 0.044 -1.060077e+02 6.369006e+01 1.508185e+01 9.676343e-02 -0 rs3885710 0 2 C T 0.029 6.908315e+01 7.476742e+01 1.490523e+01 3.560241e-01 -0 rs3923989 0 3 G A 0.208 1.425102e+01 3.165766e+01 1.501490e+01 6.528245e-01 -0 rs3928422 0 15 T C 0.476 7.669558e+00 2.578491e+01 1.496195e+01 7.662732e-01 -0 rs3929758 0 0 C A 0.276 6.095513e+00 2.862785e+01 1.482282e+01 8.314895e-01 -0 rs3963196 0 6 C G 0.110 -4.132618e+01 4.205020e+01 1.458302e+01 3.262739e-01 -0 rs3990898 0 19 T C 0.475 1.210375e+01 2.665857e+01 1.482063e+01 6.500400e-01 -0 rs4000844 0 3 C T 0.324 1.305142e+01 2.718158e+01 1.482681e+01 6.313630e-01 -0 rs449837 0 2 C T 0.120 -1.854300e+01 3.883986e+01 1.482784e+01 6.333072e-01 -0 rs5749531 0 6 C T 0.270 -1.860765e+01 2.882072e+01 1.438566e+01 5.188645e-01 -0 rs828748 0 13 A T 0.469 -8.225675e+00 2.509246e+01 1.490868e+01 7.432132e-01 -0 rs9620258 0 18 T C 0.465 3.346972e+01 2.711623e+01 1.491335e+01 2.177710e-01 -0 rs9625253 0 2 C G 0.166 5.663989e+01 3.361768e+01 1.453813e+01 9.275658e-02 -1 rs4040617 819184 0 G A 0.129 -6.893390e+01 3.809609e+01 1.475634e+01 7.108365e-02 -1 rs4075116 1043551 3 G A 0.303 1.647354e+01 2.721051e+01 1.495971e+01 5.452292e-01 -1 rs10907175 1170649 2 C A 0.104 -6.110439e-01 4.170067e+01 1.483898e+01 9.883158e-01 -1 rs6603781 1198553 9 A G 0.104 5.062098e+01 4.514516e+01 1.491001e+01 2.627961e-01 -1 rs6685064 1251214 1 T C 0.072 -2.780089e+01 4.939713e+01 1.482850e+01 5.738653e-01 -1 rs1695824 1450836 7 G T 0.242 5.386828e+01 3.030474e+01 1.476389e+01 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rs2840528 2316057 3 G A 0.434 1.209219e+01 2.603078e+01 1.480055e+01 6.425027e-01 -1 rs7545940 2331788 1 C T 0.344 -4.040628e+01 2.780182e+01 1.468452e+01 1.468594e-01 -1 rs10910060 2335072 10 A G 0.223 3.874450e+01 3.091159e+01 1.466587e+01 2.107502e-01 -1 rs4648633 2352863 4 C T 0.232 -4.779012e+01 3.083863e+01 1.487421e+01 1.219618e-01 -1 rs12023660 2389971 11 T C 0.102 3.449007e+01 4.279978e+01 1.484861e+01 4.207818e-01 -1 rs7512269 2450786 7 T C 0.124 -8.923525e+00 3.994253e+01 1.488074e+01 8.233244e-01 -1 rs2246732 2482555 4 C T 0.228 2.027621e+01 3.185534e+01 1.481628e+01 5.247874e-01 -1 rs2985862 2484730 6 A G 0.236 -2.511441e+01 3.059901e+01 1.461329e+01 4.122437e-01 -1 rs3122922 2488364 1 T C 0.201 -2.268773e+01 3.192467e+01 1.470526e+01 4.776820e-01 -1 rs10910093 2537874 1 T C 0.129 -2.610509e+01 3.954803e+01 1.476189e+01 5.095565e-01 -1 rs4486391 2545216 3 T A 0.483 -9.088419e+00 2.701707e+01 1.492888e+01 7.367387e-01 -1 rs10910097 2553591 11 T C 0.192 -2.731993e+01 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2874394 14 A G 0.324 -1.734814e+01 2.846867e+01 1.392952e+01 5.426004e-01 -1 rs2606414 2890304 7 T C 0.301 1.704726e+01 2.898365e+01 1.477040e+01 5.567318e-01 -1 rs6659552 2902616 8 C G 0.245 -1.705238e+00 2.990699e+01 1.485462e+01 9.545576e-01 -1 rs10909855 2931544 4 T C 0.128 1.973449e+01 4.083656e+01 1.474449e+01 6.291632e-01 -1 rs17391750 2932527 12 A G 0.112 1.162354e+01 4.421929e+01 1.478237e+01 7.927849e-01 -1 rs6661908 2973490 2 A G 0.189 2.115759e+01 3.474291e+01 1.468034e+01 5.428658e-01 -1 694027 2973527 13 T G 0.174 -4.716344e+00 3.670933e+01 1.487448e+01 8.978314e-01 -1 rs10489588 2974990 1 T C 0.207 1.470510e+01 3.345922e+01 1.478514e+01 6.605277e-01 -1 rs9661525 2975996 7 G T 0.187 1.846639e+01 3.500353e+01 1.471338e+01 5.980815e-01 -1 rs12409277 2980756 9 C T 0.187 1.899793e+01 3.477185e+01 1.472073e+01 5.851055e-01 -1 rs6665853 3004997 5 A G 0.297 -4.912183e+00 2.829675e+01 1.480495e+01 8.622662e-01 -1 rs7525173 3019352 12 C G 0.470 7.676359e-02 2.630550e+01 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rs4828744 151925407 4 G A 0.070 6.633532e+02 5.537957e+02 8.364750e-01 2.316507e-01 +23 rs4828747 151929154 8 C T 0.074 8.191338e+02 5.461813e+02 6.878073e-01 1.344224e-01 +23 rs2008144 151966996 4 A G 0.069 6.653272e+02 5.622074e+02 8.150273e-01 2.373045e-01 +23 rs5925336 151987489 20 T C 0.189 5.057982e+02 3.782736e+02 1.091805e+00 1.818978e-01 +23 rs1894342 151987996 11 G A 0.066 7.920495e+02 5.760390e+02 7.318519e-01 1.698581e-01 +23 rs1557505 151992064 2 G A 0.181 4.906312e+02 3.758148e+02 1.107522e+00 1.924245e-01 +23 rs5924813 151995603 7 C T 0.060 1.050542e+03 6.060025e+02 5.676362e-01 8.372142e-02 +23 rs2012435 152010745 2 T C 0.068 7.649911e+02 5.614145e+02 7.160548e-01 1.737259e-01 +23 rs2012436 152010777 2 G C 0.068 7.649911e+02 5.614145e+02 7.160548e-01 1.737259e-01 +23 rs5925368 152033116 13 G A 0.056 4.850721e+02 6.443881e+02 1.060616e+00 4.520085e-01 +23 rs6627772 152053967 5 A G 0.327 -7.348535e+02 3.037732e+02 1.913365e+00 1.597861e-02 +23 rs995423 152085362 13 A T 0.488 -2.302553e+01 2.949064e+02 1.418232e+00 9.378032e-01 +23 rs1894354 152089815 0 T C 0.177 -8.651713e+01 3.852254e+02 1.493356e+00 8.224075e-01 +23 rs5986911 152351829 6 T A 0.036 -6.052153e+02 8.346069e+02 1.458641e+00 4.687590e-01 +23 rs5945145 152351894 5 C T 0.405 2.556045e+00 2.973697e+02 1.405507e+00 9.931459e-01 +23 rs4898424 152360329 16 G T 0.274 8.014956e+01 3.346344e+02 1.358128e+00 8.108226e-01 +23 rs4898428 152397543 12 A G 0.134 -5.622230e+02 4.425575e+02 1.452369e+00 2.046388e-01 +23 rs3761536 152427138 16 A T 0.178 -2.451683e+02 3.896597e+02 1.624546e+00 5.295654e-01 +23 rs5987140 152521101 20 C T 0.111 3.357028e+01 4.930577e+02 1.405850e+00 9.457493e-01 +23 rs2266887 152760433 8 T G 0.203 4.527955e+02 3.696201e+02 1.055914e+00 2.212426e-01 +23 rs7884370 152843727 5 G A 0.041 6.650459e+02 7.275102e+02 1.254241e+00 3.611618e-01 +23 rs1734791 152851766 13 T A 0.158 1.818275e+01 4.075201e+02 1.393589e+00 9.644327e-01 +23 rs766420 153075250 6 C G 0.220 -1.161442e+02 3.563688e+02 1.374410e+00 7.446527e-01 +23 rs766419 153075507 6 C T 0.219 -2.020163e+02 3.563200e+02 1.364275e+00 5.710461e-01 +23 rs2239467 153076140 14 G A 0.224 -1.279868e+02 3.576258e+02 1.367731e+00 7.206114e-01 +23 rs4898494 153174968 5 T A 0.108 4.589111e+02 4.725147e+02 1.486027e+00 3.319961e-01 +23 rs4898348 153450097 18 T C 0.231 1.085220e+03 3.552855e+02 1.654826e+00 2.396195e-03 +23 rs5945109 153471452 8 G A 0.377 5.977579e+02 3.064267e+02 1.532848e+00 5.174515e-02 +23 rs5945122 153737610 8 C A 0.135 3.680298e+01 4.337705e+02 1.429719e+00 9.324251e-01 +23 rs2051161 153849554 3 G C 0.383 7.052883e+02 3.026393e+02 1.477207e+00 2.024911e-02 +23 3885427 154017791 18 G A 0.232 -2.548193e+02 3.451999e+02 1.424038e+00 4.608131e-01 +23 rs475025 154048640 3 G A 0.243 -2.337655e+02 3.345153e+02 1.458479e+00 4.850476e-01 +23 rs6420603 154316683 14 G A 0.029 -1.355348e+02 8.962687e+02 1.416665e+00 8.798730e-01 +23 rs574386 154411192 9 C T 0.240 -3.510010e+02 3.367436e+02 1.408866e+00 2.978471e-01 diff --git a/web/gemma/output/HLC_output.log.txt b/web/gemma/output/HLC_output.log.txt index 9dd3d75b..e8107112 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 = -3121.45 -## MLE log-likelihood in the null model = -3127.35 -## pve estimate in the null model = 0.830303 -## se(pve) in the null model = 0.108674 -## vg estimate in the null model = 347865 -## ve estimate in the null model = 23515.2 -## beta estimate in the null model = 454.076 -## se(beta) = 7.42097 +## 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 ## ## Computation Time: -## total computation time = 2.67 min +## total computation time = 2.5965 min ## computation time break down: ## time on eigen-decomposition = 0.0015 min -## time on calculating UtX = 0.4125 min -## time on optimization = 2.10517 min +## time on calculating UtX = 0.414167 min +## time on optimization = 2.03267 min ## -- cgit v1.2.3