[Genabel-commits] r1517 - in pkg/ProbABEL/checks: . R-tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 30 15:43:27 CET 2013
Author: lckarssen
Date: 2013-12-30 15:43:27 +0100 (Mon, 30 Dec 2013)
New Revision: 1517
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:
Reverting previous ProbABEL commit, which contained too many files.
Modified: pkg/ProbABEL/checks/Makefile.am
===================================================================
--- pkg/ProbABEL/checks/Makefile.am 2013-12-30 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/Makefile.am 2013-12-30 14:43:27 UTC (rev 1517)
@@ -38,12 +38,6 @@
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 =
@@ -58,17 +52,6 @@
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 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/R-tests/Makefile.am 2013-12-30 14:43:27 UTC (rev 1517)
@@ -2,9 +2,9 @@
AUTOMAKE_OPTIONS = foreign color-tests
-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 \
+R_test_files = run_models_in_R_palinear.R \
+ run_models_in_R_palogist.R \
+ run_models_in_R_pacox.R \
initial_checks.R
check_SCRIPTS =
@@ -23,10 +23,11 @@
testsdir = $(pkgdatadir)/checks/R-tests
+dist_tests_DATA = $(R_test_files) $(check_SCRIPTS)
+#dist_tests_SCRIPTS = $(check_SCRIPTS)
-TESTS = $(check_SCRIPTS)
+TESTS_ENVIRONMENT = bash
-## The palogist R test still doesn't run correctly.
-XFAIL_TESTS = run_R_test_palogist.sh
-EXTRA_DIST = $(check_SCRIPTS) $(R_test_files)
+
+TESTS = $(check_SCRIPTS)
Modified: pkg/ProbABEL/checks/R-tests/run_R_test_palinear.sh
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_R_test_palinear.sh 2013-12-30 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/R-tests/run_R_test_palinear.sh 2013-12-30 14:43:27 UTC (rev 1517)
@@ -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 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R 2013-12-30 14:43:27 UTC (rev 1517)
@@ -24,7 +24,7 @@
####
cat("Running ProbABEL...\t\t\t\t")
tmp <- system(paste0("cd ", tests.path,
- "; bash srcdir=", srcdir, " test_cox.sh 2> /dev/null; cd -"),
+ "; bash 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(paste0(srcdir, "run_model_coxph.R"))
+source("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 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R 2013-12-30 14:43:27 UTC (rev 1517)
@@ -10,9 +10,6 @@
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
@@ -54,7 +51,7 @@
cat("Comparing R output with ProbABEL output\t\t")
-source(paste0(srcdir, "run_model_linear.R"))
+source("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 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R 2013-12-30 14:43:27 UTC (rev 1517)
@@ -38,10 +38,6 @@
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
####
@@ -49,7 +45,7 @@
cat("Comparing R output with ProbABEL output\t\t")
-source(paste0(srcdir, "run_model_logist.R"))
+source("run_model_logist.R")
model.fn.0 <-
"glm( chd[noNA] ~ sex[noNA] + age[noNA] + othercov[noNA], family=binomial)"
@@ -109,16 +105,10 @@
model <- glm( chd ~ sex + age + othercov + prob[, indexHet] +
prob[, indexHom], family=binomial )
smA1A2 <- summary(model)$coef[5, 1:2]
-
- if ( nrow(summary(model)$coeff) > 5 ) {
- smA1A1 <- summary(model)$coef[6, 1:2]
- } else {
- smA1A1 <- c(NaN, NaN)
- }
-
+ smA1A1 <- summary(model)$coef[6, 1:2]
lrt <- 2 * ( logLik( model ) - logLik( model.0 ) )
- rsq <- prob.2df.PA[i-2, "Rsq"]
+ rsq <- resPa2df[i-2, "Rsq"]
if( rsq < rsq.thresh) {
row <- c(rsq, NaN, NaN, NaN, NaN, NaN)
} else {
Modified: pkg/ProbABEL/checks/test_bt.sh
===================================================================
--- pkg/ProbABEL/checks/test_bt.sh 2013-12-30 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/test_bt.sh 2013-12-30 14:43:27 UTC (rev 1517)
@@ -2,30 +2,27 @@
# This script runs checks on ProbABEL's palogist module for
# binary traits.
-echo "Analysing BT..."
+echo "analysing BT"
scriptdir=$(dirname $0)
if [ -z ${srcdir} ]; then
srcdir="."
- bindir=${scriptdir}/../src/
-else
- bindir="../src/"
fi
. ${scriptdir}/run_diff.sh
-inputdir=${scriptdir}/inputfiles
-palogist=${bindir}/palogist
+inputdir=${srcdir}/inputfiles
# 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 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/test_cox.sh 2013-12-30 14:43:27 UTC (rev 1517)
@@ -7,15 +7,11 @@
if [ -z ${srcdir} ]; then
srcdir="."
- bindir=${scriptdir}/../src/
-else
- bindir="../src/"
fi
. ${scriptdir}/run_diff.sh
-inputdir=${scriptdir}/inputfiles
-pacoxph=${bindir}/pacoxph
+inputdir=${srcdir}/inputfiles
# Redirect all output to file descriptor 3 to /dev/null except if
# the first argument is "verbose" then redirect handle 3 to stdout
@@ -25,6 +21,8 @@
exec 3>&1
fi
+pacoxph=../src/pacoxph
+
$pacoxph \
-p ${inputdir}/coxph_data.txt \
-d ${inputdir}/test.mldose \
Modified: pkg/ProbABEL/checks/test_mms.sh
===================================================================
--- pkg/ProbABEL/checks/test_mms.sh 2013-12-30 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/test_mms.sh 2013-12-30 14:43:27 UTC (rev 1517)
@@ -2,30 +2,24 @@
# This script runs checks on ProbABEL's palinear module for
# quantitative traits combined with the mmscore option.
-echo "Analysis using MMScore..."
-
-scriptdir=$(dirname $0)
-
+echo "analysis using MMScore"
if [ -z ${srcdir} ]; then
srcdir="."
- bindir=${scriptdir}/../src/
-else
- bindir="../src/"
fi
-. ${scriptdir}/run_diff.sh
+. ${srcdir}/run_diff.sh
-inputdir=${scriptdir}/inputfiles
-palinear=${bindir}/palinear
+inputdir=${srcdir}/inputfiles
# 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 ${inputdir}/mmscore_gen.mlinfo \
Modified: pkg/ProbABEL/checks/test_qt.sh
===================================================================
--- pkg/ProbABEL/checks/test_qt.sh 2013-12-30 14:39:35 UTC (rev 1516)
+++ pkg/ProbABEL/checks/test_qt.sh 2013-12-30 14:43:27 UTC (rev 1517)
@@ -2,30 +2,27 @@
# This script runs checks on ProbABEL's palinear module for
# quantitative traits.
-echo "Analysing QT..."
+echo "analysing QT"
scriptdir=$(dirname $0)
if [ -z ${srcdir} ]; then
srcdir="."
- bindir=${scriptdir}/../src/
-else
- bindir="../src/"
fi
. ${scriptdir}/run_diff.sh
-inputdir=${scriptdir}/inputfiles
-palinear=${bindir}/palinear
+inputdir=${srcdir}/inputfiles
# 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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