[Genabel-commits] r913 - pkg/ProbABEL/examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jun 10 21:15:17 CEST 2012
Author: lckarssen
Date: 2012-06-10 21:15:17 +0200 (Sun, 10 Jun 2012)
New Revision: 913
Modified:
pkg/ProbABEL/examples/Makefile.am
pkg/ProbABEL/examples/example_bt.sh
pkg/ProbABEL/examples/example_cox.sh
pkg/ProbABEL/examples/example_mms.sh
pkg/ProbABEL/examples/example_qt.sh
Log:
ProbABEL: modifications to the test scripts.
Modified: pkg/ProbABEL/examples/Makefile.am
===================================================================
--- pkg/ProbABEL/examples/Makefile.am 2012-06-05 07:52:53 UTC (rev 912)
+++ pkg/ProbABEL/examples/Makefile.am 2012-06-10 19:15:17 UTC (rev 913)
@@ -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: pkg/ProbABEL/examples/example_bt.sh
===================================================================
--- pkg/ProbABEL/examples/example_bt.sh 2012-06-05 07:52:53 UTC (rev 912)
+++ pkg/ProbABEL/examples/example_bt.sh 2012-06-10 19:15:17 UTC (rev 913)
@@ -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: pkg/ProbABEL/examples/example_cox.sh
===================================================================
--- pkg/ProbABEL/examples/example_cox.sh 2012-06-05 07:52:53 UTC (rev 912)
+++ pkg/ProbABEL/examples/example_cox.sh 2012-06-10 19:15:17 UTC (rev 913)
@@ -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: pkg/ProbABEL/examples/example_mms.sh
===================================================================
--- pkg/ProbABEL/examples/example_mms.sh 2012-06-05 07:52:53 UTC (rev 912)
+++ pkg/ProbABEL/examples/example_mms.sh 2012-06-10 19:15:17 UTC (rev 913)
@@ -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: pkg/ProbABEL/examples/example_qt.sh
===================================================================
--- pkg/ProbABEL/examples/example_qt.sh 2012-06-05 07:52:53 UTC (rev 912)
+++ pkg/ProbABEL/examples/example_qt.sh 2012-06-10 19:15:17 UTC (rev 913)
@@ -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
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