From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 27 Mar 2015 20:28:51 +0000 Subject: Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files' --- web/gemma/output/HLC_output.assoc.txt | 273350 ------------------------------- web/gemma/output/HLC_output.log.txt | 28 - 2 files changed, 273378 deletions(-) delete mode 100644 web/gemma/output/HLC_output.assoc.txt delete mode 100644 web/gemma/output/HLC_output.log.txt (limited to 'web/gemma/output') diff --git a/web/gemma/output/HLC_output.assoc.txt b/web/gemma/output/HLC_output.assoc.txt deleted file mode 100644 index 962ee30a..00000000 --- a/web/gemma/output/HLC_output.assoc.txt +++ /dev/null @@ -1,273350 +0,0 @@ -chr rs ps n_miss allele1 allele0 af beta se l_remle p_wald -0 rs1155740 0 18 T C 0.274 -8.927624e+01 1.026031e+02 1.643091e+01 3.847300e-01 -0 rs1169469 0 16 T C 0.105 9.200707e+01 1.491476e+02 1.583560e+01 5.376401e-01 -0 rs11775 0 19 G A 0.327 -1.489315e+02 9.702455e+01 1.590665e+01 1.255308e-01 -0 rs1368258 0 13 T C 0.343 8.160595e+01 1.001130e+02 1.609552e+01 4.154496e-01 -0 rs1414747 0 17 A C 0.446 9.248497e+01 8.917807e+01 1.569481e+01 3.002873e-01 -0 rs1459037 0 7 G A 0.290 -9.386644e-01 9.966103e+01 1.591604e+01 9.924896e-01 -0 rs150775 0 20 T G 0.061 -2.146073e+02 1.912066e+02 1.593540e+01 2.623327e-01 -0 rs1538704 0 6 G A 0.292 -5.174857e+01 9.488451e+01 1.577911e+01 5.857750e-01 -0 rs1578301 0 0 C T 0.447 3.293481e+01 9.209531e+01 1.595064e+01 7.208078e-01 -0 rs16907085 0 1 G A 0.124 1.249005e+02 1.392221e+02 1.599469e+01 3.701568e-01 -0 rs16992891 0 3 T C 0.333 -6.977747e+01 9.374774e+01 1.599852e+01 4.570997e-01 -0 rs17566573 0 20 A G 0.195 1.370863e+02 1.163727e+02 1.591232e+01 2.394583e-01 -0 rs2229935 0 1 T C 0.275 -2.270192e+02 1.006232e+02 1.573053e+01 2.456991e-02 -0 rs2230394 0 5 T C 0.098 2.579272e+02 1.549294e+02 1.577268e+01 9.668865e-02 -0 rs2230395 0 1 C A 0.101 2.609912e+02 1.525609e+02 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T C 0.103 -1.247495e+02 1.217766e+02 1.566343e+01 3.062231e-01 -23 rs3912366 149890696 10 C T 0.302 1.371152e+02 8.000020e+01 1.501284e+01 8.726963e-02 -23 rs5925493 149896918 19 C T 0.293 -1.790617e+01 8.094856e+01 1.591620e+01 8.250396e-01 -23 rs4644439 149903546 3 A T 0.283 -1.399303e+01 7.965685e+01 1.592753e+01 8.606397e-01 -23 rs3853550 149915046 4 C T 0.285 -1.320543e+01 7.977229e+01 1.592679e+01 8.685984e-01 -23 rs180486 149991156 5 A C 0.083 -6.842402e+01 1.322455e+02 1.605678e+01 6.051451e-01 -23 rs180487 149991301 4 T A 0.085 -6.709284e+01 1.316128e+02 1.609606e+01 6.104742e-01 -23 rs7878475 150001740 9 C T 0.078 2.213764e+02 1.342695e+02 1.619871e+01 9.993855e-02 -23 rs1930693 150024093 9 A C 0.322 -3.166999e+01 7.737095e+01 1.622410e+01 6.825062e-01 -23 rs1149370 150077385 5 C T 0.213 -6.588842e+01 8.854742e+01 1.596406e+01 4.572253e-01 -23 rs926046 150086290 8 G A 0.358 -4.172503e+01 7.575967e+01 1.590481e+01 5.820909e-01 -23 rs12557937 150086546 5 A G 0.052 -3.405087e+01 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8.178030e+01 1.581850e+01 5.988899e-01 -23 rs12560037 151839176 19 T C 0.331 -9.374265e+01 7.608673e+01 1.598719e+01 2.186117e-01 -23 rs2382883 151873256 3 A G 0.065 4.962433e+01 1.434923e+02 1.593669e+01 7.296396e-01 -23 rs6627738 151900925 14 C T 0.059 1.454160e+02 1.509728e+02 1.586812e+01 3.359982e-01 -23 rs4828744 151925407 4 G A 0.070 8.377843e+01 1.389327e+02 1.593464e+01 5.468208e-01 -23 rs4828747 151929154 8 C T 0.074 1.066877e+02 1.371978e+02 1.594889e+01 4.372258e-01 -23 rs2008144 151966996 4 A G 0.069 7.890449e+01 1.409684e+02 1.592538e+01 5.759572e-01 -23 rs5925336 151987489 20 T C 0.189 4.454084e+01 9.338956e+01 1.596915e+01 6.336528e-01 -23 rs1894342 151987996 11 G A 0.066 1.193728e+02 1.450988e+02 1.591428e+01 4.111400e-01 -23 rs1557505 151992064 2 G A 0.181 4.253441e+01 9.270232e+01 1.597832e+01 6.465923e-01 -23 rs5924813 151995603 7 C T 0.060 1.789484e+02 1.516085e+02 1.575204e+01 2.385282e-01 -23 rs2012435 152010745 2 T C 0.068 1.011081e+02 1.414283e+02 1.590293e+01 4.750588e-01 -23 rs2012436 152010777 2 G C 0.068 1.011081e+02 1.414283e+02 1.590293e+01 4.750588e-01 -23 rs5925368 152033116 13 G A 0.056 5.376141e+01 1.609354e+02 1.591488e+01 7.385023e-01 -23 rs6627772 152053967 5 A G 0.327 -1.864113e+02 7.490601e+01 1.562485e+01 1.320654e-02 -23 rs995423 152085362 13 A T 0.488 -6.090244e+01 7.253517e+01 1.593372e+01 4.015900e-01 -23 rs1894354 152089815 0 T C 0.177 -4.725626e+01 9.573306e+01 1.615418e+01 6.218258e-01 -23 rs5986911 152351829 6 T A 0.036 -2.349732e+02 2.052692e+02 1.608473e+01 2.529747e-01 -23 rs5945145 152351894 5 C T 0.405 -2.296156e+01 7.337206e+01 1.600948e+01 7.544745e-01 -23 rs4898424 152360329 16 G T 0.274 4.684036e+00 8.221131e+01 1.594832e+01 9.545914e-01 -23 rs4898428 152397543 12 A G 0.134 -5.955819e+01 1.092205e+02 1.596693e+01 5.858318e-01 -23 rs3761536 152427138 16 A T 0.178 -2.681676e+00 9.622300e+01 1.595431e+01 9.777794e-01 -23 rs5987140 152521101 20 C T 0.111 5.193335e+01 1.213441e+02 1.595543e+01 6.688794e-01 -23 rs2266887 152760433 8 T G 0.203 7.718603e+01 9.181158e+01 1.588840e+01 4.009886e-01 -23 rs7884370 152843727 5 G A 0.041 2.460087e+02 1.782285e+02 1.583888e+01 1.682200e-01 -23 rs1734791 152851766 13 T A 0.158 -1.149214e+01 1.001773e+02 1.603198e+01 9.087229e-01 -23 rs766420 153075250 6 C G 0.220 6.280638e+01 8.755395e+01 1.608354e+01 4.735554e-01 -23 rs766419 153075507 6 C T 0.219 4.411589e+01 8.756093e+01 1.602046e+01 6.146413e-01 -23 rs2239467 153076140 14 G A 0.224 5.717691e+01 8.783936e+01 1.606658e+01 5.154461e-01 -23 rs4898494 153174968 5 T A 0.108 2.427077e+02 1.155737e+02 1.590925e+01 3.631549e-02 -23 rs4898348 153450097 18 T C 0.231 2.775226e+02 8.732649e+01 1.621495e+01 1.591316e-03 -23 rs5945109 153471452 8 G A 0.377 1.691606e+02 7.536096e+01 1.619144e+01 2.530292e-02 -23 rs5945122 153737610 8 C A 0.135 1.924957e+01 1.071433e+02 1.598439e+01 8.575037e-01 -23 rs2051161 153849554 3 G C 0.383 1.635377e+02 7.466881e+01 1.599425e+01 2.905430e-02 -23 3885427 154017791 18 G A 0.232 -4.297558e+01 8.482810e+01 1.569159e+01 6.126845e-01 -23 rs475025 154048640 3 G A 0.243 -2.214191e+01 8.269887e+01 1.592490e+01 7.890283e-01 -23 rs6420603 154316683 14 G A 0.029 -8.620842e+01 2.205232e+02 1.595658e+01 6.960472e-01 -23 rs574386 154411192 9 C T 0.240 -4.051368e+01 8.233156e+01 1.565906e+01 6.229171e-01 diff --git a/web/gemma/output/HLC_output.log.txt b/web/gemma/output/HLC_output.log.txt deleted file mode 100644 index fc7975f4..00000000 --- a/web/gemma/output/HLC_output.log.txt +++ /dev/null @@ -1,28 +0,0 @@ -## -## GEMMA Version = 0.94 -## -## Command Line Input = -bfile HLC -k output_HLC.cXX.txt -lmm 1 -o HLC_output -## -## Summary Statistics: -## number of total individuals = 427 -## number of analyzed individuals = 427 -## number of covariates = 1 -## number of phenotypes = 1 -## number of total SNPs = 358499 -## number of analyzed SNPs = 273349 -## REMLE log-likelihood in the null model = -3650.56 -## MLE log-likelihood in the null model = -3657.67 -## pve estimate in the null model = 0.840196 -## se(pve) in the null model = 0.106606 -## vg estimate in the null model = 4.2245e+06 -## ve estimate in the null model = 265756 -## beta estimate in the null model = 1202.14 -## se(beta) = 24.9475 -## -## Computation Time: -## total computation time = 2.73533 min -## computation time break down: -## time on eigen-decomposition = 0.00166667 min -## time on calculating UtX = 0.417333 min -## time on optimization = 2.146 min -## -- cgit v1.2.3