From 759a7a23b0ea848b8c8ffe2804841322254d8696 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Mon, 5 May 2014 17:09:24 +0000 Subject: Committing a bunch of changes related to integrating GEMMA and adding the correlation matrix page --- web/gemma/CANDLE.fam | 1505 + web/gemma/HLC.bed | Bin 0 -> 38359396 bytes web/gemma/HLC.bim | 358499 ++++++++++++++++++++ web/gemma/HLC.fam | 427 + web/gemma/HLC.map | 358520 +++++++++++++++++++++ web/gemma/gemma | Bin 0 -> 6161970 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 + 11 files changed, 992942 insertions(+) create mode 100644 web/gemma/CANDLE.fam create mode 100755 web/gemma/HLC.bed create mode 100755 web/gemma/HLC.bim create mode 100755 web/gemma/HLC.fam create mode 100755 web/gemma/HLC.map create mode 100755 web/gemma/gemma create mode 100644 web/gemma/output/HLC_output.assoc.txt create mode 100644 web/gemma/output/HLC_output.log.txt create mode 100755 web/gemma/output_HLC.cXX.txt create mode 100755 web/gemma/tmp_pheno/BXD_1436869_at_9Jbx12ev.txt create mode 100755 web/gemma/tmp_pheno/test.txt (limited to 'web/gemma') diff --git a/web/gemma/CANDLE.fam b/web/gemma/CANDLE.fam new file mode 100644 index 00000000..558122c6 --- /dev/null +++ b/web/gemma/CANDLE.fam @@ -0,0 +1,1505 @@ +CAN0001_1 CAN0001_1 0 0 0 x +CAN0002_1 CAN0002_1 0 0 0 x +CAN0003_1 CAN0003_1 0 0 0 x +CAN0004_1 CAN0004_1 0 0 0 x +CAN0005_1 CAN0005_1 0 0 0 x +CAN0006_1 CAN0006_1 0 0 0 x +CAN0007_1 CAN0007_1 0 0 0 x +CAN0008_1 CAN0008_1 0 0 0 x +CAN0009_1 CAN0009_1 0 0 0 x +CAN0010_1 CAN0010_1 0 0 0 x +CAN0011_1 CAN0011_1 0 0 0 x +CAN0012_1 CAN0012_1 0 0 0 x +CAN0013_1 CAN0013_1 0 0 0 x +CAN0014_1 CAN0014_1 0 0 0 x +CAN0015_1 CAN0015_1 0 0 0 x +CAN0016_1 CAN0016_1 0 0 0 x +CAN0017_1 CAN0017_1 0 0 0 x +CAN0018_1 CAN0018_1 0 0 0 x +CAN0019_1 CAN0019_1 0 0 0 x 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154411192 9 C T 0.240 -3.520485e+00 2.378650e+01 1.475017e+01 8.824102e-01 diff --git a/web/gemma/output/HLC_output.log.txt b/web/gemma/output/HLC_output.log.txt new file mode 100644 index 00000000..9dd3d75b --- /dev/null +++ b/web/gemma/output/HLC_output.log.txt @@ -0,0 +1,28 @@ +## +## 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 = -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 +## +## Computation Time: +## total computation time = 2.67 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 +## diff --git a/web/gemma/output_HLC.cXX.txt b/web/gemma/output_HLC.cXX.txt new file mode 100755 index 00000000..716846c3 --- /dev/null +++ b/web/gemma/output_HLC.cXX.txt @@ -0,0 +1,427 @@ +0.2608705535 -0.0009201602878 -0.002760621771 -0.0009876281047 0.001377173127 0.0004647613414 -0.0008585932104 -0.00180097167 -0.0009423760859 -0.0007536310498 0.0005537100865 -0.002354425597 0.001605676985 -0.001291743402 -0.00391180101 0.0002140645669 0.001792605062 0.02967720343 -0.0008930191734 -0.002560295353 -0.001485503428 0.01307122992 -0.0008860618835 0.0002634223733 -0.003465110864 -0.0002708480836 -0.0006096538067 -0.002504943034 -0.002682079276 -0.0009836972396 0.0001879256994 0.0001344336418 0.001528488991 0.0004568544787 -0.001184402413 0.002127134377 -0.001503502216 0.00946908528 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