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/BXD.fam | 93 - web/gemma/CANDLE.fam | 1505 - web/gemma/HLC.bed | Bin 38359396 -> 0 bytes web/gemma/HLC.bim | 358499 -------------------- web/gemma/HLC.fam | 427 - web/gemma/HLC.map | 358520 --------------------- web/gemma/gemma | Bin 6161970 -> 0 bytes web/gemma/output/HLC_output.assoc.txt | 273350 ---------------- web/gemma/output/HLC_output.log.txt | 28 - web/gemma/output_HLC.cXX.txt | 427 - web/gemma/tmp_pheno/BXD_1436869_at_9Jbx12ev.txt | 93 - web/gemma/tmp_pheno/test.txt | 93 - 12 files changed, 993035 deletions(-) delete mode 100644 web/gemma/BXD.fam delete mode 100644 web/gemma/CANDLE.fam delete mode 100755 web/gemma/HLC.bed delete mode 100755 web/gemma/HLC.bim delete mode 100755 web/gemma/HLC.fam delete mode 100755 web/gemma/HLC.map delete mode 100755 web/gemma/gemma delete mode 100644 web/gemma/output/HLC_output.assoc.txt delete mode 100644 web/gemma/output/HLC_output.log.txt delete mode 100755 web/gemma/output_HLC.cXX.txt delete mode 100755 web/gemma/tmp_pheno/BXD_1436869_at_9Jbx12ev.txt delete mode 100755 web/gemma/tmp_pheno/test.txt (limited to 'web/gemma') diff --git a/web/gemma/BXD.fam b/web/gemma/BXD.fam deleted file mode 100644 index 31e89482..00000000 --- a/web/gemma/BXD.fam +++ /dev/null @@ -1,93 +0,0 @@ -BXD1 BXD1 0 0 0 10.512 -BXD2 BXD2 0 0 0 9.882 -BXD5 BXD5 0 0 0 11.388 -BXD6 BXD6 0 0 0 10.453 -BXD8 BXD8 0 0 0 10.486 -BXD9 BXD9 0 0 0 10.503 -BXD11 BXD11 0 0 0 11.619 -BXD12 BXD12 0 0 0 11.227 -BXD13 BXD13 0 0 0 10.444 -BXD14 BXD14 0 0 0 x -BXD15 BXD15 0 0 0 11.050 -BXD16 BXD16 0 0 0 10.252 -BXD18 BXD18 0 0 0 x -BXD19 BXD19 0 0 0 11.235 -BXD20 BXD20 0 0 0 10.321 -BXD21 BXD21 0 0 0 10.486 -BXD22 BXD22 0 0 0 10.854 -BXD23 BXD23 0 0 0 11.175 -BXD24a BXD24a 0 0 0 x -BXD24 BXD24 0 0 0 10.560 -BXD25 BXD25 0 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rs6641395 147153698 5 C A 0.436 -2.018470e+00 7.241221e+01 1.595161e+01 9.777752e-01 -23 rs4843992 147154934 14 T C 0.432 8.706183e+00 7.338863e+01 1.601742e+01 9.056236e-01 -23 rs16994558 147157673 17 A G 0.105 -5.788726e+01 1.197030e+02 1.586361e+01 6.289254e-01 -23 rs5936353 147191530 12 G A 0.401 8.802462e+01 7.490215e+01 1.590027e+01 2.405748e-01 -23 rs2335519 147195057 21 G T 0.398 6.827980e+01 7.595261e+01 1.596117e+01 3.691728e-01 -23 rs6540370 147227273 21 G A 0.495 -5.139438e+01 7.308184e+01 1.477624e+01 4.822886e-01 -23 rs3860290 147236307 10 C T 0.487 2.682473e+01 7.336196e+01 1.574655e+01 7.148089e-01 -23 rs5936392 147333595 11 G T 0.286 3.184495e+01 8.138690e+01 1.599904e+01 6.957874e-01 -23 rs5936214 147352571 18 A T 0.263 7.221601e+01 8.382988e+01 1.629852e+01 3.894710e-01 -23 rs10521874 147364274 17 T C 0.260 7.188296e+01 8.506796e+01 1.606021e+01 3.985827e-01 -23 rs5936216 147364327 2 C A 0.271 7.996266e+01 8.207828e+01 1.612163e+01 3.304993e-01 -23 rs6641437 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-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 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