[Genabel-commits] r1516 - in pkg/ProbABEL/checks: . R-tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 30 15:39:36 CET 2013
Author: lckarssen
Date: 2013-12-30 15:39:35 +0100 (Mon, 30 Dec 2013)
New Revision: 1516
Modified:
pkg/ProbABEL/checks/Makefile.am
pkg/ProbABEL/checks/R-tests/Makefile.am
pkg/ProbABEL/checks/R-tests/run_R_test_palinear.sh
pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R
pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R
pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R
pkg/ProbABEL/checks/test_bt.sh
pkg/ProbABEL/checks/test_cox.sh
pkg/ProbABEL/checks/test_mms.sh
pkg/ProbABEL/checks/test_qt.sh
Log:
The basic ProbABEL test scripts can now also be run from a different directory than the one they are in.
Modified: pkg/ProbABEL/checks/Makefile.am
===================================================================
--- pkg/ProbABEL/checks/Makefile.am 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/Makefile.am 2013-12-30 14:39:35 UTC (rev 1516)
@@ -38,6 +38,12 @@
input_files = $(phenofiles) $(genofiles) run_diff.sh test_all.sh
+# R_test_files = R-tests/run_models_in_R_palinear.R R-tests/run_model_linear.R \
+# R-tests/run_models_in_R_palogist.R R-tests/run_model_logist.R \
+# R-tests/run_models_in_R_pacox.R R-tests/run_model_coxph.R \
+# R-tests/initial_checks.R
+
+
check_SCRIPTS =
@@ -52,6 +58,17 @@
check_SCRIPTS += test_cox.sh
endif
+# if HAVE_R
+# if BUILD_palinear
+# check_SCRIPTS += R-tests/run_R_test_palinear.sh
+# endif
+# if BUILD_palogist
+# #check_SCRIPTS += R-tests/run_R_test_palogist.sh
+# endif
+# if BUILD_pacoxph
+# check_SCRIPTS += R-tests/run_R_test_pacox.sh
+# endif
+# endif
TESTS = $(check_SCRIPTS)
Modified: pkg/ProbABEL/checks/R-tests/Makefile.am
===================================================================
--- pkg/ProbABEL/checks/R-tests/Makefile.am 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/R-tests/Makefile.am 2013-12-30 14:39:35 UTC (rev 1516)
@@ -2,9 +2,9 @@
AUTOMAKE_OPTIONS = foreign color-tests
-R_test_files = run_models_in_R_palinear.R \
- run_models_in_R_palogist.R \
- run_models_in_R_pacox.R \
+R_test_files = run_models_in_R_palinear.R run_model_linear.R \
+ run_models_in_R_palogist.R run_model_logist.R \
+ run_models_in_R_pacox.R run_model_coxph.R \
initial_checks.R
check_SCRIPTS =
@@ -23,11 +23,10 @@
testsdir = $(pkgdatadir)/checks/R-tests
-dist_tests_DATA = $(R_test_files) $(check_SCRIPTS)
-#dist_tests_SCRIPTS = $(check_SCRIPTS)
-TESTS_ENVIRONMENT = bash
+TESTS = $(check_SCRIPTS)
+## The palogist R test still doesn't run correctly.
+XFAIL_TESTS = run_R_test_palogist.sh
-
-TESTS = $(check_SCRIPTS)
+EXTRA_DIST = $(check_SCRIPTS) $(R_test_files)
Modified: pkg/ProbABEL/checks/R-tests/run_R_test_palinear.sh
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_R_test_palinear.sh 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/R-tests/run_R_test_palinear.sh 2013-12-30 14:39:35 UTC (rev 1516)
@@ -7,5 +7,5 @@
if [ -z ${srcdir} ]; then
srcdir="."
fi
-
+echo "SRCDIR=$srcdir"
$Rcommand -f ${srcdir}/run_models_in_R_palinear.R --args ${srcdir}/
Modified: pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R 2013-12-30 14:39:35 UTC (rev 1516)
@@ -24,7 +24,7 @@
####
cat("Running ProbABEL...\t\t\t\t")
tmp <- system(paste0("cd ", tests.path,
- "; bash test_cox.sh 2> /dev/null; cd -"),
+ "; bash srcdir=", srcdir, " test_cox.sh 2> /dev/null; cd -"),
intern=TRUE)
cat("OK\n")
@@ -54,7 +54,7 @@
cat("Comparing R output with ProbABEL output\t\t")
-source("run_model_coxph.R")
+source(paste0(srcdir, "run_model_coxph.R"))
model.fn.0 <-
"coxph( Surv(fupt_chd, chd)[noNA] ~ sex[noNA] + age[noNA] + othercov[noNA] )"
Modified: pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R 2013-12-30 14:39:35 UTC (rev 1516)
@@ -10,6 +10,9 @@
pheno.file <- "height.txt"
source(paste0(srcdir, "initial_checks.R"))
+cat("IN R SRCDIR=", srcdir, "\n")
+cat("IN R tests.path=", tests.path, "\n")
+cat("In R inputfiles.path=", inputfiles.path, "\n")
####
## Run ProbABEL to get the output data we want to compare/verify
@@ -51,7 +54,7 @@
cat("Comparing R output with ProbABEL output\t\t")
-source("run_model_linear.R")
+source(paste0(srcdir, "run_model_linear.R"))
model.fn.0 <- "lm( height[noNA] ~ sex[noNA] + age[noNA] )"
model.fn <- "lm( height ~ sex + age + snp )"
Modified: pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R 2013-12-30 14:39:35 UTC (rev 1516)
@@ -38,6 +38,10 @@
paste0(tests.path, "logist_prob_2df.out.txt"),
head=TRUE)[, cols2df]
+## Fix chi^2 for the case that there is no variation (SNP 6 in the
+## info file). ProbABEL lists it as NaN, R lists it as:
+prob.dom.PA[6, 4] <- 0.0
+
####
## run analysis in R
####
@@ -45,7 +49,7 @@
cat("Comparing R output with ProbABEL output\t\t")
-source("run_model_logist.R")
+source(paste0(srcdir, "run_model_logist.R"))
model.fn.0 <-
"glm( chd[noNA] ~ sex[noNA] + age[noNA] + othercov[noNA], family=binomial)"
@@ -105,10 +109,16 @@
model <- glm( chd ~ sex + age + othercov + prob[, indexHet] +
prob[, indexHom], family=binomial )
smA1A2 <- summary(model)$coef[5, 1:2]
- smA1A1 <- summary(model)$coef[6, 1:2]
+
+ if ( nrow(summary(model)$coeff) > 5 ) {
+ smA1A1 <- summary(model)$coef[6, 1:2]
+ } else {
+ smA1A1 <- c(NaN, NaN)
+ }
+
lrt <- 2 * ( logLik( model ) - logLik( model.0 ) )
- rsq <- resPa2df[i-2, "Rsq"]
+ rsq <- prob.2df.PA[i-2, "Rsq"]
if( rsq < rsq.thresh) {
row <- c(rsq, NaN, NaN, NaN, NaN, NaN)
} else {
Modified: pkg/ProbABEL/checks/test_bt.sh
===================================================================
--- pkg/ProbABEL/checks/test_bt.sh 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/test_bt.sh 2013-12-30 14:39:35 UTC (rev 1516)
@@ -2,27 +2,30 @@
# This script runs checks on ProbABEL's palogist module for
# binary traits.
-echo "analysing BT"
+echo "Analysing BT..."
scriptdir=$(dirname $0)
if [ -z ${srcdir} ]; then
srcdir="."
+ bindir=${scriptdir}/../src/
+else
+ bindir="../src/"
fi
. ${scriptdir}/run_diff.sh
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+palogist=${bindir}/palogist
# Redirect all output to file descriptor 3 to /dev/null except if
# the first argument is "verbose" then redirect handle 3 to stdout
exec 3>/dev/null
if [ "$1" = "verbose" ]; then
+ echo "Verbose mode ON"
exec 3>&1
fi
-palogist=../src/palogist
-
$palogist \
-p ${inputdir}/logist_data.txt \
-d ${inputdir}/test.mldose \
Modified: pkg/ProbABEL/checks/test_cox.sh
===================================================================
--- pkg/ProbABEL/checks/test_cox.sh 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/test_cox.sh 2013-12-30 14:39:35 UTC (rev 1516)
@@ -7,11 +7,15 @@
if [ -z ${srcdir} ]; then
srcdir="."
+ bindir=${scriptdir}/../src/
+else
+ bindir="../src/"
fi
. ${scriptdir}/run_diff.sh
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+pacoxph=${bindir}/pacoxph
# Redirect all output to file descriptor 3 to /dev/null except if
# the first argument is "verbose" then redirect handle 3 to stdout
@@ -21,8 +25,6 @@
exec 3>&1
fi
-pacoxph=../src/pacoxph
-
$pacoxph \
-p ${inputdir}/coxph_data.txt \
-d ${inputdir}/test.mldose \
Modified: pkg/ProbABEL/checks/test_mms.sh
===================================================================
--- pkg/ProbABEL/checks/test_mms.sh 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/test_mms.sh 2013-12-30 14:39:35 UTC (rev 1516)
@@ -2,24 +2,30 @@
# This script runs checks on ProbABEL's palinear module for
# quantitative traits combined with the mmscore option.
-echo "analysis using MMScore"
+echo "Analysis using MMScore..."
+
+scriptdir=$(dirname $0)
+
if [ -z ${srcdir} ]; then
srcdir="."
+ bindir=${scriptdir}/../src/
+else
+ bindir="../src/"
fi
-. ${srcdir}/run_diff.sh
+. ${scriptdir}/run_diff.sh
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+palinear=${bindir}/palinear
# Redirect all output to file descriptor 3 to /dev/null except if
# the first argument is "verbose" then redirect handle 3 to stdout
exec 3>/dev/null
if [ "$1" = "verbose" ]; then
+ echo "Verbose mode ON"
exec 3>&1
fi
-palinear=../src/palinear
-
$palinear \
-p ${inputdir}/mmscore_pheno.PHE \
-i ${inputdir}/mmscore_gen.mlinfo \
Modified: pkg/ProbABEL/checks/test_qt.sh
===================================================================
--- pkg/ProbABEL/checks/test_qt.sh 2013-12-30 13:33:53 UTC (rev 1515)
+++ pkg/ProbABEL/checks/test_qt.sh 2013-12-30 14:39:35 UTC (rev 1516)
@@ -2,27 +2,30 @@
# This script runs checks on ProbABEL's palinear module for
# quantitative traits.
-echo "analysing QT"
+echo "Analysing QT..."
scriptdir=$(dirname $0)
if [ -z ${srcdir} ]; then
srcdir="."
+ bindir=${scriptdir}/../src/
+else
+ bindir="../src/"
fi
. ${scriptdir}/run_diff.sh
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+palinear=${bindir}/palinear
# Redirect all output to file descriptor 3 to /dev/null except if
# the first argument is "verbose" then redirect handle 3 to stdout
exec 3>/dev/null
if [ "$1" = "verbose" ]; then
+ echo "Verbose mode ON"
exec 3>&1
fi
-palinear="../src/palinear"
-
echo "base analysis"
$palinear \
-p ${inputdir}/height.txt \
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