[Genabel-commits] r1199 - pkg/ProbABEL/examples

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-04-26 08:23:11 +0200 (Fri, 26 Apr 2013)
New Revision: 1199

Modified:
   pkg/ProbABEL/examples/example_bt.sh
   pkg/ProbABEL/examples/example_mms.sh
Log:
Enabled the prob vs. dose and prob_fv vs. dose_fv checks in the BT example test script of ProbABEL. 
These tests in the MMS script are still disabled because the LogLik column is missing in the prob output, which results in diff giving and error, even when the values of beta and se_beta are the same. 



Modified: pkg/ProbABEL/examples/example_bt.sh
===================================================================
--- pkg/ProbABEL/examples/example_bt.sh	2013-04-25 18:33:26 UTC (rev 1198)
+++ pkg/ProbABEL/examples/example_bt.sh	2013-04-26 06:23:11 UTC (rev 1199)
@@ -65,9 +65,12 @@
         "BT check ($model model): prob vs. prob_fv"
 done
 
-# 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
+run_diff logist_prob_add.out.txt \
+    logist_add.out.txt \
+    "BT check: prob vs. dose" \
+    -I beta_SNP
+
+run_diff logist_prob_fv_add.out.txt \
+    logist_fv_add.out.txt \
+    "BT check: prob_fv vs. dose_fv" \
+    -I beta_SNP

Modified: pkg/ProbABEL/examples/example_mms.sh
===================================================================
--- pkg/ProbABEL/examples/example_mms.sh	2013-04-25 18:33:26 UTC (rev 1198)
+++ pkg/ProbABEL/examples/example_mms.sh	2013-04-26 06:23:11 UTC (rev 1199)
@@ -64,10 +64,14 @@
         "mmscore check ($model model): prob vs. prob_fv"
 done
 
-# 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
+# The following checks are disabled because of the missing LogLik
+# column in the prob data
+# run_diff mmscore_prob_add.out.txt \
+#     mmscore_add.out.txt \
+#     "mmscore check: prob vs. dose" \
+#     -I beta_SNP
 
-# echo "mmscore check: prob_fv vs. dose_fv"
-# diff mmscore_prob_fv_add.out.txt mmscore_fv_add.out.txt
+# run_diff mmscore_prob_fv_add.out.txt \
+#     mmscore_fv_add.out.txt \
+#     "mmscore check: prob_fv vs. dose_fv" \
+#     -I beta_SNP