[Genabel-commits] r987 - branches/ProbABEL-refactoring/ProbABEL/examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 24 12:27:26 CEST 2012
Author: lckarssen
Date: 2012-10-24 12:27:25 +0200 (Wed, 24 Oct 2012)
New Revision: 987
Added:
branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_InvSigma_aj.sex.age.small.dat
branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_gen.small.mldose
branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_pheno.small.PHE
Modified:
branches/ProbABEL-refactoring/ProbABEL/examples/Makefile.am
branches/ProbABEL-refactoring/ProbABEL/examples/example_bt.sh
branches/ProbABEL-refactoring/ProbABEL/examples/example_cox.sh
branches/ProbABEL-refactoring/ProbABEL/examples/example_mms.sh
branches/ProbABEL-refactoring/ProbABEL/examples/example_qt.sh
Log:
In ProbABEL-refactoring branch: merged examples with trunk. Again an easy one, since the examples hadn't changed since the branch was created.
Modified: branches/ProbABEL-refactoring/ProbABEL/examples/Makefile.am
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/Makefile.am 2012-10-24 10:18:55 UTC (rev 986)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/Makefile.am 2012-10-24 10:27:25 UTC (rev 987)
@@ -50,7 +50,12 @@
TESTS = $(check_SCRIPTS)
-cleanfiles_bt = logist_add.out.txt logist_fv_add.out.txt
+cleanfiles_bt = logist_add.out.txt logist_fv_add.out.txt \
+logist_prob_2df.out.txt logist_prob_fv_2df.out.txt \
+logist_prob_fv_domin.out.txt logist_prob_add.out.txt \
+logist_prob_fv_add.out.txt logist_prob_over_domin.out.txt \
+logist_prob_domin.out.txt logist_prob_fv_recess.out.txt \
+logist_prob_fv_over_domin.out.txt logist_prob_recess.out.txt
cleanfiles_qt = height_base_add.out.txt height_base_fv_add.out.txt \
height_allcov_add.out.txt height_allcov_fv_add.out.txt \
Modified: branches/ProbABEL-refactoring/ProbABEL/examples/example_bt.sh
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/example_bt.sh 2012-10-24 10:18:55 UTC (rev 986)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/example_bt.sh 2012-10-24 10:27:25 UTC (rev 987)
@@ -19,4 +19,33 @@
-c 19 \
-o logist_fv
+echo "BT check: dose vs. dose_fv"
diff logist_add.out.txt logist_fv_add.out.txt
+
+../src/palogist \
+ -p ${srcdir}/logist_data.txt \
+ -d ${srcdir}/test.mlprob \
+ -i ${srcdir}/test.mlinfo \
+ -m ${srcdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o logist_prob
+
+../src/palogist \
+ -p ${srcdir}/logist_data.txt \
+ -d ${srcdir}/test.prob.fvi \
+ -i ${srcdir}/test.mlinfo \
+ -m ${srcdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o logist_prob_fv
+
+echo "BT check: prob vs. prob_fv"
+diff logist_prob_add.out.txt logist_prob_fv_add.out.txt
+
+# Commented out because of slightly different output formats. We need
+# something smart here.
+# echo "BT check: prob vs. dose"
+# diff logist_prob_add.out.txt logist_add.out.txt
+# echo "BT check: prob_fv vs. dose_fv"
+# diff logist_prob_fv_add.out.txt logist_fv_add.out.txt
Modified: branches/ProbABEL-refactoring/ProbABEL/examples/example_cox.sh
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/example_cox.sh 2012-10-24 10:18:55 UTC (rev 986)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/example_cox.sh 2012-10-24 10:27:25 UTC (rev 987)
@@ -10,12 +10,27 @@
-m ${srcdir}/test.map \
-c 19 \
-o coxph
-../src/pacoxph \
- -p ${srcdir}/coxph_data.txt \
- -d ${srcdir}/test.dose.fvi \
- -i ${srcdir}/test.mlinfo \
- -m ${srcdir}/test.map \
- -c 19 \
- -o coxph_fv
-diff coxph_add.out.txt coxph_fv_add.out.txt
+# ../src/pacoxph \
+# -p ${srcdir}/coxph_data.txt \
+# -d ${srcdir}/test.dose.fvi \
+# -i ${srcdir}/test.mlinfo \
+# -m ${srcdir}/test.map \
+# -c 19 \
+# -o coxph_fv
+
+# echo "pacoxph check: dose vs. dose_fv"
+# diff coxph_add.out.txt coxph_fv_add.out.txt
+
+
+# ../src/pacoxph \
+# -p ${srcdir}/coxph_data.txt \
+# -d ${srcdir}/test.mlprob \
+# -i ${srcdir}/test.mlinfo \
+# -m ${srcdir}/test.map \
+# --ngpreds=2 \
+# -c 19 \
+# -o coxph_prob
+
+# echo "pacoxph check: dose vs. prob"
+# diff coxph_add.out.txt coxph_prob_add.out.txt
Modified: branches/ProbABEL-refactoring/ProbABEL/examples/example_mms.sh
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/example_mms.sh 2012-10-24 10:18:55 UTC (rev 986)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/example_mms.sh 2012-10-24 10:27:25 UTC (rev 987)
@@ -7,16 +7,19 @@
-p ${srcdir}/mmscore_pheno.PHE \
-i ${srcdir}/mmscore_gen.mlinfo \
-d ${srcdir}/mmscore_gen.mldose \
- --sep="," -o mmscore \
+ --sep="," \
+ -o mmscore \
--mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
../src/palinear \
-p ${srcdir}/mmscore_pheno.PHE \
-i ${srcdir}/mmscore_gen.mlinfo \
-d ${srcdir}/mmscore_gen.dose.fvi \
- --sep="," -o mmscore_fv \
+ --sep="," \
+ -o mmscore_fv \
--mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+echo "mmscore check: dose vs. dose_fv"
diff mmscore_add.out.txt mmscore_fv_add.out.txt
@@ -24,14 +27,25 @@
-p ${srcdir}/mmscore_pheno.PHE \
-i ${srcdir}/mmscore_gen.mlinfo \
-d ${srcdir}/mmscore_gen.mlprob \
- --ngpreds=2 --sep="," -o mmscore_prob \
+ --ngpreds=2 --sep="," \
+ -o mmscore_prob \
--mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
../src/palinear \
-p ${srcdir}/mmscore_pheno.PHE \
-i ${srcdir}/mmscore_gen.mlinfo \
-d ${srcdir}/mmscore_gen.prob.fvi \
- --ngpreds=2 --sep="," -o mmscore_prob_fv \
+ --ngpreds=2 --sep="," \
+ -o mmscore_prob_fv \
--mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+echo "mmscore check: prob vs. prob_fv"
diff mmscore_prob_add.out.txt mmscore_prob_fv_add.out.txt
+
+# Commented out because of slightly different output formats. We need
+# something smart here.
+# echo "mmscore check: prob vs. dose"
+# diff mmscore_prob_add.out.txt mmscore_add.out.txt
+
+# echo "mmscore check: prob_fv vs. dose_fv"
+# diff mmscore_prob_fv_add.out.txt mmscore_fv_add.out.txt
Modified: branches/ProbABEL-refactoring/ProbABEL/examples/example_qt.sh
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/example_qt.sh 2012-10-24 10:18:55 UTC (rev 986)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/example_qt.sh 2012-10-24 10:27:25 UTC (rev 987)
@@ -20,6 +20,7 @@
-c 19 \
-o height_base_fv
+echo "QT check: dose vs. dose_fv"
diff height_base_add.out.txt height_base_fv_add.out.txt
@@ -38,6 +39,7 @@
-c 19 --allcov \
-o height_allcov_fv
+echo "QT check: allcov: dose vs. dose_fv"
diff height_allcov_add.out.txt height_allcov_fv_add.out.txt
@@ -57,6 +59,7 @@
-c 19 --interaction=1 \
-o height_int1_fv
+echo "QT check: interactions: dose vs. dose_fv"
diff height_int1_add.out.txt height_int1_fv_add.out.txt
@@ -76,6 +79,7 @@
-c 19 --robust \
-o height_robust_fv
+echo "QT check: robust: dose vs. dose_fv"
diff height_robust_add.out.txt height_robust_fv_add.out.txt
@@ -95,6 +99,7 @@
-c 19 --robust --interaction=1 \
-o height_robust_int1_fv
+echo "QT check: robust & interaction: dose vs. dose_fv"
diff height_robust_int1_add.out.txt height_robust_int1_fv_add.out.txt
@@ -114,6 +119,7 @@
-c 19 --ngp=2 \
-o height_ngp2_fv
+echo "QT check: prob vs. prob_fv"
diff height_ngp2_add.out.txt height_ngp2_fv_add.out.txt
diff height_ngp2_domin.out.txt height_ngp2_fv_domin.out.txt
diff height_ngp2_over_domin.out.txt height_ngp2_fv_over_domin.out.txt
Copied: branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_InvSigma_aj.sex.age.small.dat (from rev 986, pkg/ProbABEL/examples/mmscore_InvSigma_aj.sex.age.small.dat)
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_InvSigma_aj.sex.age.small.dat (rev 0)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_InvSigma_aj.sex.age.small.dat 2012-10-24 10:27:25 UTC (rev 987)
@@ -0,0 +1,10 @@
+id4 0.0182686989332702 -1.85665437227337e-05 3.53271468398681e-05 -1.74067659984958e-05 7.43017952446252e-05 -4.50104634347183e-06 -0.000124985264981788 3.3678291247208e-05 5.91968582288439e-05 -0.000243645201364358
+id10 -1.85665437227311e-05 0.0182033225536506 -1.97096076622397e-05 -5.96162563595784e-05 -5.4476919601606e-05 -9.50226926118848e-05 8.62259783546112e-05 7.3858364200391e-05 3.10831766033596e-05 -0.000130544230147021
+id25 3.53271468398634e-05 -1.97096076622424e-05 0.0181688614380818 8.52863460066612e-05 -2.43025930791677e-05 2.81566776967037e-05 4.85600196715389e-06 -6.56752842697857e-06 -1.78033754378254e-05 -1.72662880972169e-05
+id33 -1.74067659984974e-05 -5.96162563595756e-05 8.52863460066646e-05 0.0181194433068409 -5.18411780980829e-05 1.50204770703661e-05 8.56024933212197e-06 4.86573389645691e-05 3.91817984047859e-05 2.79910558167308e-05
+id35 7.43017952446215e-05 -5.44769196016117e-05 -2.43025930791681e-05 -5.18411780980874e-05 0.018106435724767 2.19056691758357e-05 -0.000128600049471664 7.17399863803957e-06 -4.24308810003088e-05 -9.37329781039098e-06
+id58 -4.50104634347325e-06 -9.50226926118893e-05 2.81566776967108e-05 1.50204770703701e-05 2.19056691758332e-05 0.0179881874374435 -1.17277182399346e-05 -4.99197036924978e-05 5.71784745599148e-05 7.8067768163972e-05
+id68 -0.000124985264981788 8.62259783546178e-05 4.85600196715395e-06 8.56024933212903e-06 -0.000128600049471660 -1.17277182399364e-05 0.0181586089581595 2.04445273957100e-05 9.39041676761655e-05 2.69629411670812e-05
+id74 3.36782912472085e-05 7.38583642003905e-05 -6.56752842698657e-06 4.86573389645756e-05 7.17399863804557e-06 -4.99197036925027e-05 2.04445273957019e-05 0.0179962093643653 -0.000143202021910123 -0.000129318612519593
+id107 5.91968582288441e-05 3.10831766033532e-05 -1.78033754378163e-05 3.91817984047789e-05 -4.2430881000305e-05 5.71784745599093e-05 9.3904167676175e-05 -0.000143202021910134 0.0182122458019134 -8.89499732951819e-05
+id119 -0.000243645201364356 -0.000130544230147016 -1.72662880972305e-05 2.79910558167332e-05 -9.37329781039559e-06 7.80677681639793e-05 2.69629411670782e-05 -0.000129318612519587 -8.89499732951819e-05 0.0183196994000799
Copied: branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_gen.small.mldose (from rev 986, pkg/ProbABEL/examples/mmscore_gen.small.mldose)
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_gen.small.mldose (rev 0)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_gen.small.mldose 2012-10-24 10:27:25 UTC (rev 987)
@@ -0,0 +1,10 @@
+1->id4 MLDOSE 1 0 2 0 1
+1->id10 MLDOSE 2 2 1 2 0
+1->id25 MLDOSE 1 2 0 2 0
+1->id33 MLDOSE NaN 0 2 0 0
+1->id35 MLDOSE 1 0 0 0 0
+1->id58 MLDOSE 2 1 NaN 0 0
+1->id68 MLDOSE 0 1 1 0 1
+1->id74 MLDOSE 1 0 0 0 0
+1->id107 MLDOSE 1 0 NaN 1 0
+1->id119 MLDOSE 2 1 0 0 0
Copied: branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_pheno.small.PHE (from rev 986, pkg/ProbABEL/examples/mmscore_pheno.small.PHE)
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_pheno.small.PHE (rev 0)
+++ branches/ProbABEL-refactoring/ProbABEL/examples/mmscore_pheno.small.PHE 2012-10-24 10:27:25 UTC (rev 987)
@@ -0,0 +1,11 @@
+id height_residuals
+id4 -9.8130684563732
+id10 -3.47642823404311
+id25 6.26095765925731
+id33 11.3778459732314
+id35 -4.79095430879806
+id58 0.370774680307449
+id68 -8.65341409945518
+id74 4.95199124661318
+id107 -9.8280719102797
+id119 -2.05732829257249
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