[Genabel-commits] r1345 - pkg/ProbABEL/examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 16 15:51:12 CEST 2013
Author: lckarssen
Date: 2013-10-16 15:51:12 +0200 (Wed, 16 Oct 2013)
New Revision: 1345
Modified:
pkg/ProbABEL/examples/Makefile.am
pkg/ProbABEL/examples/example_bt.sh
pkg/ProbABEL/examples/example_cox.sh
pkg/ProbABEL/examples/example_qt.sh
Log:
Fixes in ProbABEL's examples:
- in the .sh scripts (except mmscore) an old variable ${inputdir} was still present. That is now replaced by ${gtdatadir}, as it should
- Makefile.am: Added rule and variables to clean up after running the examples (make clean now does what you would expect).
Modified: pkg/ProbABEL/examples/Makefile.am
===================================================================
--- pkg/ProbABEL/examples/Makefile.am 2013-10-07 22:31:37 UTC (rev 1344)
+++ pkg/ProbABEL/examples/Makefile.am 2013-10-16 13:51:12 UTC (rev 1345)
@@ -40,3 +40,84 @@
gdatadir = $(pkgdatadir)/examples/gtdata
dist_gdata_DATA = $(genofiles)
+
+
+cleanfiles_example_qt = height_allcov_fv_add.out.txt \
+ height_base_add.out.txt \
+ height_base_fv_add.out.txt \
+ height_int1_fv_add.out.txt \
+ height_ngp2_2df.out.txt \
+ height_ngp2_add.out.txt \
+ height_ngp2_allcov_fv_2df.out.txt \
+ height_ngp2_allcov_fv_add.out.txt \
+ height_ngp2_allcov_fv_domin.out.txt \
+ height_ngp2_allcov_fv_over_domin.out.txt \
+ height_ngp2_allcov_fv_recess.out.txt \
+ height_ngp2_domin.out.txt \
+ height_ngp2_fv_2df.out.txt \
+ height_ngp2_fv_add.out.txt \
+ height_ngp2_fv_domin.out.txt \
+ height_ngp2_fv_over_domin.out.txt \
+ height_ngp2_fv_recess.out.txt \
+ height_ngp2_int1_fv_2df.out.txt \
+ height_ngp2_int1_fv_add.out.txt \
+ height_ngp2_int1_fv_domin.out.txt \
+ height_ngp2_int1_fv_over_domin.out.txt \
+ height_ngp2_int1_fv_recess.out.txt \
+ height_ngp2_over_domin.out.txt \
+ height_ngp2_recess.out.txt \
+ height_ngp2_robust_fv_2df.out.txt \
+ height_ngp2_robust_fv_add.out.txt \
+ height_ngp2_robust_fv_domin.out.txt \
+ height_ngp2_robust_fv_over_domin.out.txt \
+ height_ngp2_robust_fv_recess.out.txt \
+ height_ngp2_robust_int1_fv_2df.out.txt \
+ height_ngp2_robust_int1_fv_add.out.txt \
+ height_ngp2_robust_int1_fv_domin.out.txt \
+ height_ngp2_robust_int1_fv_over_domin.out.txt \
+ height_ngp2_robust_int1_fv_recess.out.txt \
+ height_robust_fv_add.out.txt \
+ height_robust_int1_fv_add.out.txt
+
+cleanfiles_example_bt = logist_add.out.txt \
+ logist_fv_add.out.txt \
+ logist_prob_2df.out.txt \
+ logist_prob_add.out.txt \
+ logist_prob_domin.out.txt \
+ logist_prob_fv_2df.out.txt \
+ logist_prob_fv_add.out.txt \
+ logist_prob_fv_domin.out.txt \
+ logist_prob_fv_over_domin.out.txt \
+ logist_prob_fv_recess.out.txt \
+ logist_prob_over_domin.out.txt \
+ logist_prob_recess.out.txt
+
+cleanfiles_example_cox = coxph_dose_add.out.txt \
+ coxph_dose_fv_add.out.txt \
+ coxph_prob_2df.out.txt \
+ coxph_prob_add.out.txt \
+ coxph_prob_domin.out.txt \
+ coxph_prob_fv_2df.out.txt \
+ coxph_prob_fv_add.out.txt \
+ coxph_prob_fv_domin.out.txt \
+ coxph_prob_fv_over_domin.out.txt \
+ coxph_prob_fv_recess.out.txt \
+ coxph_prob_over_domin.out.txt \
+ coxph_prob_recess.out.txt
+
+cleanfiles_example_mmscore = mmscore_dose_add.out.txt \
+ mmscore_dose_fv_add.out.txt \
+ mmscore_prob_2df.out.txt \
+ mmscore_prob_add.out.txt \
+ mmscore_prob_domin.out.txt \
+ mmscore_prob_fv_2df.out.txt \
+ mmscore_prob_fv_add.out.txt \
+ mmscore_prob_fv_domin.out.txt \
+ mmscore_prob_fv_over_domin.out.txt \
+ mmscore_prob_fv_recess.out.txt \
+ mmscore_prob_over_domin.out.txt \
+ mmscore_prob_recess.out.txt
+
+
+CLEANFILES = $(cleanfiles_example_qt) $(cleanfiles_example_bt) \
+ $(cleanfiles_example_cox) $(cleanfiles_example_mmscore)
Modified: pkg/ProbABEL/examples/example_bt.sh
===================================================================
--- pkg/ProbABEL/examples/example_bt.sh 2013-10-07 22:31:37 UTC (rev 1344)
+++ pkg/ProbABEL/examples/example_bt.sh 2013-10-16 13:51:12 UTC (rev 1345)
@@ -15,9 +15,9 @@
# Using text-based dosage genotype files as input
${padir}palogist \
-p logist_data.txt \
- -d ${inputdir}/test.mldose \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.mldose \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 \
-o logist
@@ -25,9 +25,9 @@
# Using filevector (DatABEL) files as dosage genotype input
${padir}palogist \
-p logist_data.txt \
- -d ${inputdir}/test.dose.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.dose.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 \
-o logist_fv
@@ -35,9 +35,9 @@
# Using text-based probability files as genotype input
${padir}palogist \
-p logist_data.txt \
- -d ${inputdir}/test.mlprob \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.mlprob \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
--ngpreds=2 \
-c 19 \
-o logist_prob
@@ -46,9 +46,9 @@
# Using filevector (DatABEL) probability files as genotype input
${padir}palogist \
-p logist_data.txt \
- -d ${inputdir}/test.prob.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.prob.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
--ngpreds=2 \
-c 19 \
-o logist_prob_fv
Modified: pkg/ProbABEL/examples/example_cox.sh
===================================================================
--- pkg/ProbABEL/examples/example_cox.sh 2013-10-07 22:31:37 UTC (rev 1344)
+++ pkg/ProbABEL/examples/example_cox.sh 2013-10-16 13:51:12 UTC (rev 1345)
@@ -14,9 +14,9 @@
# Using text-based dosage genotype files as input
${padir}pacoxph \
-p coxph_data.txt \
- -d ${inputdir}/test.mldose \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.mldose \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 \
-o coxph_dose
@@ -24,9 +24,9 @@
# Using filevector (DatABEL) files as dosage genotype input
${padir}pacoxph \
-p coxph_data.txt \
- -d ${inputdir}/test.dose.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.dose.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 \
-o coxph_dose_fv
@@ -34,9 +34,9 @@
# Using text-based probability files as genotype input
${padir}pacoxph \
-p coxph_data.txt \
- -d ${inputdir}/test.mlprob \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.mlprob \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
--ngpreds=2 \
-c 19 \
-o coxph_prob
@@ -45,9 +45,9 @@
# Using filevector (DatABEL) probability files as genotype input
${padir}pacoxph \
-p coxph_data.txt \
- -d ${inputdir}/test.prob.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.prob.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
--ngpreds=2 \
-c 19 \
-o coxph_prob_fv
Modified: pkg/ProbABEL/examples/example_qt.sh
===================================================================
--- pkg/ProbABEL/examples/example_qt.sh 2013-10-07 22:31:37 UTC (rev 1344)
+++ pkg/ProbABEL/examples/example_qt.sh 2013-10-16 13:51:12 UTC (rev 1345)
@@ -16,9 +16,9 @@
echo "basic analysis"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.mldose \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.mldose \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 \
-o height_base
@@ -26,9 +26,9 @@
# Using filevector (DatABEL) files as dosage genotype input
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.dose.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.dose.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 \
-o height_base_fv
@@ -36,9 +36,9 @@
echo "Option --allcov"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.dose.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.dose.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --allcov \
-o height_allcov_fv
@@ -46,9 +46,9 @@
echo "Option --interaction=1"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.dose.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.dose.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --interaction=1 \
-o height_int1_fv
@@ -56,9 +56,9 @@
echo "Option --robust"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.dose.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.dose.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --robust \
-o height_robust_fv
@@ -66,9 +66,9 @@
echo "Option --robust --interaction=1"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.dose.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.dose.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --robust --interaction=1 \
-o height_robust_int1_fv
@@ -77,9 +77,9 @@
echo "Option --ngp=2, mlprob file"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.mlprob \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.mlprob \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --ngp=2 \
-o height_ngp2
@@ -87,9 +87,9 @@
# Using filevector (DatABEL) probability files as genotype input
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.prob.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.prob.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --ngp=2 \
-o height_ngp2_fv
@@ -97,9 +97,9 @@
echo "Option --ngp=2 --allcov"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.prob.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.prob.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --ngp=2 --allcov \
-o height_ngp2_allcov_fv
@@ -107,9 +107,9 @@
echo "Option --ngp=2 --interaction=1"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.prob.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.prob.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --ngp=2 --interaction=1 \
-o height_ngp2_int1_fv
@@ -117,9 +117,9 @@
echo "Option --ngp=2 --robust"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.prob.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.prob.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --ngp=2 --robust \
-o height_ngp2_robust_fv
@@ -127,8 +127,8 @@
echo "Option --ngp=2 --robust --interaction=1"
${padir}palinear \
-p height.txt \
- -d ${inputdir}/test.prob.fvi \
- -i ${inputdir}/test.mlinfo \
- -m ${inputdir}/test.map \
+ -d ${gtdatadir}/test.prob.fvi \
+ -i ${gtdatadir}/test.mlinfo \
+ -m ${gtdatadir}/test.map \
-c 19 --ngp=2 --robust --interaction=1 \
-o height_ngp2_robust_int1_fv
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