[Genabel-commits] r1902 - in branches/ProbABEL-pvals/ProbABEL: . checks checks/R-tests checks/inputfiles checks/verified_results doc examples/gtdata src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 29 22:43:04 CET 2014
Author: lckarssen
Date: 2014-12-29 22:43:04 +0100 (Mon, 29 Dec 2014)
New Revision: 1902
Added:
branches/ProbABEL-pvals/ProbABEL/checks/check_pacoxph_nocovar.sh
branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/README
branches/ProbABEL-pvals/ProbABEL/src/invsigma.cpp
branches/ProbABEL-pvals/ProbABEL/src/invsigma.h
branches/ProbABEL-pvals/ProbABEL/src/mlinfo.cpp
branches/ProbABEL-pvals/ProbABEL/src/mlinfo.h
Removed:
branches/ProbABEL-pvals/ProbABEL/src/data.cpp
branches/ProbABEL-pvals/ProbABEL/src/data.h
Modified:
branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am
branches/ProbABEL-pvals/ProbABEL/checks/R-tests/initial_checks.R
branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_pacox.R
branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palinear.R
branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palogist.R
branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.map
branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.mldose
branches/ProbABEL-pvals/ProbABEL/checks/test_mms.sh
branches/ProbABEL-pvals/ProbABEL/checks/test_qt.sh
branches/ProbABEL-pvals/ProbABEL/checks/verified_results/height_add.out.txt
branches/ProbABEL-pvals/ProbABEL/checks/verified_results/height_base_add.out.txt
branches/ProbABEL-pvals/ProbABEL/checks/verified_results/height_ngp2_2df.out.txt
branches/ProbABEL-pvals/ProbABEL/checks/verified_results/height_ngp2_add.out.txt
branches/ProbABEL-pvals/ProbABEL/checks/verified_results/height_ngp2_domin.out.txt
branches/ProbABEL-pvals/ProbABEL/checks/verified_results/height_ngp2_over_domin.out.txt
branches/ProbABEL-pvals/ProbABEL/checks/verified_results/height_ngp2_recess.out.txt
branches/ProbABEL-pvals/ProbABEL/configure.ac
branches/ProbABEL-pvals/ProbABEL/doc/ChangeLog
branches/ProbABEL-pvals/ProbABEL/doc/Doxyfile.in
branches/ProbABEL-pvals/ProbABEL/doc/INSTALL
branches/ProbABEL-pvals/ProbABEL/doc/Makefile.am
branches/ProbABEL-pvals/ProbABEL/doc/ProbABEL_manual.tex
branches/ProbABEL-pvals/ProbABEL/doc/pacoxph.1
branches/ProbABEL-pvals/ProbABEL/doc/palinear.1
branches/ProbABEL-pvals/ProbABEL/doc/palogist.1
branches/ProbABEL-pvals/ProbABEL/doc/probabel.1
branches/ProbABEL-pvals/ProbABEL/examples/gtdata/test.map
branches/ProbABEL-pvals/ProbABEL/src/Makefile.am
branches/ProbABEL-pvals/ProbABEL/src/coxph_data.cpp
branches/ProbABEL-pvals/ProbABEL/src/coxph_data.h
branches/ProbABEL-pvals/ProbABEL/src/gendata.cpp
branches/ProbABEL-pvals/ProbABEL/src/main.cpp
branches/ProbABEL-pvals/ProbABEL/src/main_functions_dump.cpp
branches/ProbABEL-pvals/ProbABEL/src/main_functions_dump.h
branches/ProbABEL-pvals/ProbABEL/src/phedata.cpp
branches/ProbABEL-pvals/ProbABEL/src/reg1.cpp
branches/ProbABEL-pvals/ProbABEL/src/reg1.h
branches/ProbABEL-pvals/ProbABEL/src/regdata.cpp
Log:
Merged the changes in ProbABEL trunk into the ProbABEL-pvals branch.
This includes the v0.4.4 fixes in the Cox PH module.
Done using the command:
svn merge -r r1721:1901 ^/pkg/ProbABEL
NOTE: this version compiles, but the checks (still) fail because the p-values haven't been fully incorporated in the checks yet.
Modified: branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am 2014-12-29 21:43:04 UTC (rev 1902)
@@ -49,13 +49,17 @@
check_SCRIPTS += test_bt.sh
endif
if BUILD_pacoxph
-check_SCRIPTS += test_cox.sh
+check_SCRIPTS += test_cox.sh check_pacoxph_nocovar.sh
endif
AM_TESTS_ENVIRONMENT= \
PA_BINDIR=$(top_builddir)/src
TESTS = $(check_SCRIPTS)
+## The pacoxph nocovar test doesn't run correctly until bug #1266 is
+## fixed.
+XFAIL_TESTS = check_pacoxph_nocovar.sh
+
EXTRA_DIST = $(verified_results) $(input_files) $(check_SCRIPTS)
@@ -118,11 +122,13 @@
mmscore_prob_recess.out.txt mmscore_prob_add.out.txt \
mmscore_prob_2df.out.txt mmscore_prob_fv_2df.out.txt
-cleanfiles_cox = coxph_dose_add.out.txt coxph_dose_fv_add.out.txt \
-coxph_prob_fv_over_domin.out.txt coxph_prob_fv_domin.out.txt \
-coxph_prob_over_domin.out.txt coxph_prob_fv_add.out.txt \
-coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
-coxph_prob_recess.out.txt coxph_prob_add.out.txt \
+cleanfiles_cox = pacoxph_nocovar_add.out.txt \
+coxph_data.txt \
+coxph_dose_add.out.txt coxph_dose_fv_add.out.txt \
+coxph_prob_fv_over_domin.out.txt coxph_prob_fv_domin.out.txt \
+coxph_prob_over_domin.out.txt coxph_prob_fv_add.out.txt \
+coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
+coxph_prob_recess.out.txt coxph_prob_add.out.txt \
coxph_prob_2df.out.txt coxph_prob_fv_2df.out.txt
Modified: branches/ProbABEL-pvals/ProbABEL/checks/R-tests/initial_checks.R
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/R-tests/initial_checks.R 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/R-tests/initial_checks.R 2014-12-29 21:43:04 UTC (rev 1902)
@@ -11,6 +11,13 @@
## look for the variables freq and poly.
rsq.thresh <- 1e-16
+## A function that prints text with empty space following it. Used to
+## print what is tested (to be followed with an OK if all is OK).
+prnt <- function(string) {
+ cat(sprintf("%-50s", string))
+}
+
+
####
## load the data
####
@@ -28,7 +35,7 @@
idNames <- dose[, 1]
idNames <- sub("[0-9]+->", "", idNames)
dose[, 1] <- idNames
-cat("Dose: check consistency of names\t\t")
+prnt("Dose: check consistency of names")
stopifnot( all.equal(dose[, 1], pheno[, 1], tol) )
cat("OK\n")
@@ -39,7 +46,7 @@
idNames <- prob[, 1]
idNames <- sub("[0-9]+->", "", idNames)
prob[, 1] <- idNames
-cat("Prob: check consistency of names\t\t")
+prnt("Prob: check consistency of names")
stopifnot( all.equal(prob[, 1], pheno[, 1], tol) )
cat("OK\n")
@@ -50,7 +57,7 @@
indexHet <- indexHom + 1
doseFromProb[, i] <- prob[, indexHom] * 2 + prob[, indexHet]
}
-cat("Check consistency dose <-> prob gtdata\t\t")
+prnt("Check consistency dose <-> prob gtdata")
stopifnot( all.equal(dose[, 3:ncol(dose)],
as.data.frame(doseFromProb)[,3:ncol(doseFromProb)],
tol=tol )
Modified: branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_pacox.R
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_pacox.R 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_pacox.R 2014-12-29 21:43:04 UTC (rev 1902)
@@ -25,7 +25,7 @@
####
## Run ProbABEL to get the output data we want to compare/verify
####
-cat("Running ProbABEL...\t\t\t\t")
+prnt("Running ProbABEL...")
tmp <- system(paste0("bash ", tests.path, "test_cox.sh 2> /dev/null"),
intern=TRUE)
cat("OK\n")
@@ -48,7 +48,7 @@
####
attach(pheno)
-cat("Comparing R output with ProbABEL output\t\t")
+cat("Comparing R output with ProbABEL output:\n")
source(paste0(srcdir, "run_model_coxph.R"))
@@ -57,48 +57,52 @@
model.fn <- "coxph( Surv(fupt_chd, chd) ~ sex + age + othercov + snp1 )"
## Additive model, dosages
+prnt(" additive (dosages)")
snpdose <- "dose[, i]"
dose.add.R <- run.model(model.fn.0, model.fn, snpdose)
colnames(dose.add.R) <- colsAdd
rownames(dose.add.R) <- NULL
stopifnot( all.equal(dose.add.PA, dose.add.R, tol=tol) )
-cat("additive ")
+cat("OK\n")
-
## Additive model, probabilities
+prnt(" additive (probabilities)")
snpprob <- "doseFromProb[, i]"
prob.add.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.add.R) <- colsAdd
rownames(prob.add.R) <- NULL
stopifnot( all.equal(prob.add.PA, prob.add.R, tol=tol) )
-cat("additive ")
+cat("OK\n")
## dominant model
+prnt(" dominant")
snpprob <- "prob[, indexHom] + prob[, indexHet]"
prob.dom.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.dom.R) <- colsDom
rownames(prob.dom.R) <- NULL
stopifnot( all.equal(prob.dom.PA, prob.dom.R, tol=tol) )
-cat("dominant ")
+cat("OK\n")
## recessive model
+prnt(" recessive")
snpprob <- "prob[, indexHom]"
prob.rec.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.rec.R) <- colsRec
rownames(prob.rec.R) <- NULL
stopifnot( all.equal(prob.rec.PA, prob.rec.R, tol=tol) )
-cat("recessive ")
+cat("OK\n")
## over-dominant model
+prnt(" overdominant")
snpprob <- "prob[, indexHet]"
prob.odom.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.odom.R) <- colsOdom
rownames(prob.odom.R) <- NULL
stopifnot( all.equal(prob.odom.PA, prob.odom.R, tol=tol) )
-cat("overdominant ")
+cat("OK\n")
-
## 2df model
+prnt(" 2df")
model.fn <-
"coxph( Surv(fupt_chd, chd) ~ sex + age + othercov + snp1 + snp2 )"
snpd1 <- "prob[, indexHet]"
@@ -107,6 +111,4 @@
colnames(prob.2df.R) <- cols2df
rownames(prob.2df.R) <- NULL
stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
-cat("2df\n")
-
-cat("\t\t\t\t\t\tOK\n")
+cat("OK\n")
Modified: branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palinear.R
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palinear.R 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palinear.R 2014-12-29 21:43:04 UTC (rev 1902)
@@ -14,7 +14,7 @@
####
## Run ProbABEL to get the output data we want to compare/verify
####
-cat("Running ProbABEL...\t\t\t\t")
+prnt("Running ProbABEL...")
tmp <- system(paste0("bash ", tests.path, "test_qt.sh"),
intern=TRUE)
cat("OK\n")
@@ -36,10 +36,14 @@
## (SNP 6 in the info file). ProbABEL lists them all as 0.0, R lists
## them as:
prob.dom.PA[6, 2:4] <- c(NaN, NaN, 0.0)
-#for 2df model the last SNP is interchangeable: EIGEN calculates the beta for the other SNP than R. This causes the beta to have the wrong sign. This part of change the position of the snp beta(and swaps sign) and SE if beta and other SE are 0
-if (sum(abs(prob.2df.PA[6, 2:3]))==0){
-prob.2df.PA[6, 2:3] <-c(prob.2df.PA[6, 4]*-1,prob.2df.PA[6, 5])
-prob.2df.PA[6, 4:5] <- c(NA, NA)
+
+## For the 2df model the last SNP is interchangeable: ProbABEL
+## calculates the beta for the other SNP than R. This causes the beta
+## to have the wrong sign. This part changes the position of the SNP
+## beta (and swaps sign) and SE if beta and the other SE are 0.
+if (sum(abs(prob.2df.PA[6, 2:3])) == 0){
+ prob.2df.PA[6, 2:3] <- c(prob.2df.PA[6, 4] * -1, prob.2df.PA[6, 5])
+ prob.2df.PA[6, 4:5] <- c(NA, NA)
}
####
@@ -47,7 +51,7 @@
####
attach(pheno)
-cat("Comparing R output with ProbABEL output\t\t")
+cat("Comparing R output with ProbABEL output:\n")
source(paste0(srcdir, "run_model_linear.R"))
@@ -55,47 +59,53 @@
model.fn <- "lm( height ~ sex + age + snp )"
## Additive model, dosages
+prnt(" additive (dosages)")
snpdose <- "dose[, i]"
dose.add.R <- run.model(model.fn.0, model.fn, snpdose)
colnames(dose.add.R) <- colsAdd
rownames(dose.add.R) <- NULL
stopifnot( all.equal(dose.add.PA, dose.add.R, tol=tol) )
-cat("additive ")
+cat("OK\n")
-
## Additive model, probabilities
+prnt(" additive (probabilities)")
snpprob <- "doseFromProb[, i]"
prob.add.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.add.R) <- colsAdd
rownames(prob.add.R) <- NULL
stopifnot( all.equal(prob.add.PA, prob.add.R, tol=tol) )
-cat("additive ")
+cat("OK\n")
## dominant model
+prnt(" dominant")
snpprob <- "prob[, indexHom] + prob[, indexHet]"
prob.dom.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.dom.R) <- colsDom
rownames(prob.dom.R) <- NULL
stopifnot( all.equal(prob.dom.PA, prob.dom.R, tol=tol) )
-cat("dominant ")
+cat("OK\n")
## recessive model
+prnt(" recessive")
snpprob <- "prob[, indexHom]"
prob.rec.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.rec.R) <- colsRec
rownames(prob.rec.R) <- NULL
stopifnot( all.equal(prob.rec.PA, prob.rec.R, tol=tol) )
-cat("recessive ")
+#print("OK", justify="right")
+cat("OK\n")
## over-dominant model
+prnt(" overdominant")
snpprob <- "prob[, indexHet]"
prob.odom.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.odom.R) <- colsOdom
rownames(prob.odom.R) <- NULL
stopifnot( all.equal(prob.odom.PA, prob.odom.R, tol=tol) )
-cat("overdominant ")
+cat("OK\n")
## 2df model
+prnt(" 2df")
prob.2df.R <- data.frame()
for (i in 3:dim(dose)[2]) {
indexHom <- 3 + ( i - 3 ) * 2
@@ -127,8 +137,5 @@
}
colnames(prob.2df.R) <- cols2df
rownames(prob.2df.R) <- NULL
-
stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
-cat("2df\n")
-
-cat("\t\t\t\t\t\tOK\n")
+cat("OK\n")
Modified: branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palogist.R
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palogist.R 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/R-tests/run_models_in_R_palogist.R 2014-12-29 21:43:04 UTC (rev 1902)
@@ -14,7 +14,7 @@
####
## Run ProbABEL to get the output data we want to compare/verify
####
-cat("Running ProbABEL...\t\t\t\t")
+prnt("Running ProbABEL...")
tmp <- system(paste0("bash ", tests.path, "test_bt.sh"),
intern=TRUE)
cat("OK\n")
@@ -41,7 +41,7 @@
####
attach(pheno)
-cat("Comparing R output with ProbABEL output\t\t")
+cat("Comparing R output with ProbABEL output\n")
source(paste0(srcdir, "run_model_logist.R"))
@@ -50,47 +50,52 @@
model.fn <- "glm( chd ~ sex + age + othercov + snp, family=binomial )"
## Additive model, dosages
+prnt(" additive (dosages)")
snpdose <- "dose[, i]"
dose.add.R <- run.model(model.fn.0, model.fn, snpdose)
colnames(dose.add.R) <- colsAdd
rownames(dose.add.R) <- NULL
stopifnot( all.equal(dose.add.PA, dose.add.R, tol=tol) )
-cat("additive ")
+cat("OK\n")
## Additive model, probabilities
+prnt(" additive (probabilities)")
snpprob <- "doseFromProb[, i]"
prob.add.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.add.R) <- colsAdd
rownames(prob.add.R) <- NULL
stopifnot( all.equal(prob.add.PA, prob.add.R, tol=tol) )
-cat("additive ")
+cat("OK\n")
## dominant model
+prnt(" dominant")
snpprob <- "prob[, indexHom] + prob[, indexHet]"
prob.dom.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.dom.R) <- colsDom
rownames(prob.dom.R) <- NULL
stopifnot( all.equal(prob.dom.PA, prob.dom.R, tol=tol) )
-cat("dominant ")
+cat("OK\n")
## recessive model
+prnt(" recessive")
snpprob <- "prob[, indexHom]"
prob.rec.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.rec.R) <- colsRec
rownames(prob.rec.R) <- NULL
stopifnot( all.equal(prob.rec.PA, prob.rec.R, tol=tol) )
-cat("recessive ")
+cat("OK\n")
## over-dominant model
+prnt(" overdominant")
snpprob <- "prob[, indexHet]"
prob.odom.R <- run.model(model.fn.0, model.fn, snpprob)
colnames(prob.odom.R) <- colsOdom
rownames(prob.odom.R) <- NULL
stopifnot( all.equal(prob.odom.PA, prob.odom.R, tol=tol) )
-cat("overdominant ")
+cat("OK\n")
-
## 2df model
+prnt(" 2df")
prob.2df.R <- data.frame()
for (i in 3:dim(dose)[2]) {
indexHom <- 3 + ( i - 3 ) * 2
@@ -124,6 +129,4 @@
colnames(prob.2df.R) <- cols2df
rownames(prob.2df.R) <- NULL
stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
-cat("2df\n")
-
-cat("\t\t\t\t\t\tOK\n")
+cat("OK\n")
Copied: branches/ProbABEL-pvals/ProbABEL/checks/check_pacoxph_nocovar.sh (from rev 1901, pkg/ProbABEL/checks/check_pacoxph_nocovar.sh)
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/check_pacoxph_nocovar.sh (rev 0)
+++ branches/ProbABEL-pvals/ProbABEL/checks/check_pacoxph_nocovar.sh 2014-12-29 21:43:04 UTC (rev 1902)
@@ -0,0 +1,46 @@
+#!/bin/bash
+# L.C. Karssen
+# This script is used to test whether the Cox PH regression works
+# correctly when no covariate is present in the phenotype input file.
+# Currently this test fails, see bug #1266.
+
+echo "Testing pacoxph without covariates..."
+
+# Exit with error when one of the steps in the script fails
+set -e
+
+# -------- Set some default paths and file names -------
+if [ -z ${srcdir} ]; then
+ srcdir="."
+fi
+inputdir="${srcdir}/inputfiles/"
+padir="${srcdir}/../src/"
+
+dosefile="$inputdir/test.mldose"
+infofile="$inputdir/test.mlinfo"
+mapfile="$inputdir/test.map"
+orig_phenofile="$inputdir/coxph_data.txt"
+phenofile="coxph_data.txt"
+outfile="pacoxph_nocovar"
+pacoxph="${padir}/pacoxph"
+
+# ------ Prepare the phenotype file be removing the covariate column
+# from the existing phenotype file ------
+awk '{print $1, $2, $3}' $orig_phenofile > $phenofile
+
+
+# ---------- function definitions ----------
+run_test ()
+{
+ ## When bug #1266 is fixed, this function should be expanded to
+ ## include a verification against known-good results.
+ echo "Checking whether Cox PH regression works without covariates..."
+ $pacoxph -p $phenofile -d $dosefile -i $infofile -m $mapfile \
+ -o $outfile
+
+}
+
+
+# ---------- Continuation of the main function ----------
+run_test
+echo "---- Finished check for Cox regression without covariates ----"
Copied: branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/README (from rev 1901, pkg/ProbABEL/checks/inputfiles/README)
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/README (rev 0)
+++ branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/README 2014-12-29 21:43:04 UTC (rev 1902)
@@ -0,0 +1,15 @@
+This README file describes the 'special' properties of the SNPs in the
+test input files, as well as any other relevant information related
+the files in the inputfiles directory.
+
+* The SNPs
+ - SNP 1: Tests multi-letter alleles (indel, e.g. from 1kG) in Al1 (bug
+ #2586).
+ - SNP 2: Tests multi-letter alleles (indel, e.g. from 1kG) in Al2 (bug
+ #2586); Tests NaN in genetic data.
+ - SNP 3:
+ - SNP 4:
+ - SNP 5: Tests low Rsq in info file.
+ - SNP 6: Tests low MAF, only one out of 200 people has a different dosage.
+
+* Other files
Modified: branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.map
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.map 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.map 2014-12-29 21:43:04 UTC (rev 1902)
@@ -1,6 +1,6 @@
rs position 0 1
-rs7247199 204938 A G
-rs8102643 207859 C T
+rs7247199 204938 A GAC
+rs8102643 207859 C TGGT
rs8102615 211970 A T
rs8105536 212033 A G
rs2312724 217034 C T
Modified: branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.mldose
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.mldose 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/inputfiles/test.mldose 2014-12-29 21:43:04 UTC (rev 1902)
@@ -1,200 +1,200 @@
1->id636728 MLDOSE 0.678 1.622 1.732 1.585 1.867 1.000
-2->id890314 MLDOSE 0.66 1.621 1.737 1.59 1.869 2.000
+2->id890314 MLDOSE 0.660 1.621 1.737 1.590 1.869 2.000
3->id102874 MLDOSE 0.684 1.623 1.731 1.585 1.866 2.000
-4->id200949 MLDOSE 0.667 NaN 1.728 1.576 1.866 2.000
-5->id336491 MLDOSE 0.66 1.609 1.737 1.577 1.869 2.000
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-7->id21999 MLDOSE 0.67 1.62 1.735 1.588 1.867 2.000
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8->id433893 MLDOSE 0.663 1.615 1.734 1.572 1.869 2.000
9->id688932 MLDOSE 0.672 1.619 1.729 1.585 1.862 2.000
-10->id394203 MLDOSE 0.666 1.619 1.729 1.58 1.863 2.000
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11->id995678 MLDOSE 0.672 1.619 1.733 1.583 1.867 2.000
-12->id694339 MLDOSE 0.666 1.615 1.733 1.59 1.869 2.000
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13->id256455 MLDOSE 0.673 1.617 1.737 1.584 1.869 2.000
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15->id817128 MLDOSE 0.666 1.609 1.735 1.589 1.868 2.000
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18->id701472 MLDOSE 0.666 1.621 1.731 1.585 1.867 2.000
19->id850010 MLDOSE 0.669 1.615 1.736 1.581 1.868 2.000
20->id268483 MLDOSE 0.669 1.618 1.732 1.582 1.865 2.000
-21->id738781 MLDOSE 0.666 1.611 1.73 1.59 1.862 2.000
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24->id751101 MLDOSE 0.669 1.624 1.738 1.589 1.869 2.000
25->id826300 MLDOSE 0.666 1.605 1.736 1.586 1.869 2.000
26->id884387 MLDOSE 0.661 1.604 1.734 1.587 1.868 2.000
27->id492414 MLDOSE 0.666 1.619 1.733 1.583 1.866 2.000
28->id268871 MLDOSE 0.669 1.621 1.731 1.576 1.869 2.000
-29->id627354 MLDOSE 0.666 1.615 1.735 1.59 1.869 2.000
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31->id163442 MLDOSE 0.675 1.621 1.737 1.586 1.869 2.000
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33->id687857 MLDOSE 0.667 1.621 1.734 1.586 1.869 2.000
-34->id871570 MLDOSE 0.666 1.61 1.731 1.576 1.864 2.000
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35->id724067 MLDOSE 0.666 1.619 1.736 1.583 1.868 2.000
36->id874076 MLDOSE 0.676 1.617 1.738 1.585 1.869 2.000
-37->id927863 MLDOSE 0.67 1.62 1.734 1.586 1.865 2.000
-38->id369805 MLDOSE 0.663 1.616 1.73 1.583 1.867 2.000
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39->id668376 MLDOSE 0.675 1.617 1.736 1.582 1.869 2.000
-40->id717362 MLDOSE 0.66 1.62 1.736 1.59 1.869 2.000
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42->id336637 MLDOSE 0.661 1.618 1.734 1.576 1.865 2.000
43->id60633 MLDOSE 0.669 1.619 1.731 1.579 1.866 2.000
44->id848600 MLDOSE 0.664 1.615 1.737 1.576 1.869 2.000
45->id169514 MLDOSE 0.664 1.615 1.737 1.583 1.869 2.000
46->id690732 MLDOSE 0.663 1.619 1.737 1.586 1.868 2.000
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51->id941921 MLDOSE 0.667 1.619 1.731 1.588 1.862 2.000
-52->id784646 MLDOSE 0.663 1.603 1.739 1.584 1.87 2.000
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53->id520954 MLDOSE 0.664 1.619 1.732 1.581 1.864 2.000
-54->id996355 MLDOSE 0.66 1.605 1.736 1.586 1.865 2.000
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55->id96730 MLDOSE 0.664 1.619 1.736 1.573 1.868 2.000
56->id673442 MLDOSE 0.666 1.609 1.735 1.575 1.867 2.000
57->id68305 MLDOSE 0.672 1.618 1.735 1.585 1.866 2.000
58->id653025 MLDOSE 0.678 1.617 1.738 1.585 1.868 2.000
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60->id335725 MLDOSE 0.666 1.616 1.714 1.593 1.845 2.000
61->id980400 MLDOSE 0.663 1.607 1.733 1.588 1.867 2.000
62->id869939 MLDOSE 0.667 1.619 1.733 1.588 1.865 2.000
-63->id297563 MLDOSE 0.673 1.614 1.72 1.585 1.866 2.000
-64->id852663 MLDOSE 0.666 1.603 1.729 1.585 1.87 2.000
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65->id162070 MLDOSE 0.666 1.619 1.728 1.572 1.868 2.000
-66->id272875 MLDOSE 0.66 1.605 1.737 1.584 1.869 2.000
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68->id422204 MLDOSE 0.663 1.615 1.734 1.576 1.867 2.000
-69->id120197 MLDOSE 0.66 1.62 1.731 1.588 1.87 2.000
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71->id803855 MLDOSE 0.669 1.616 1.732 1.586 1.865 2.000
72->id255048 MLDOSE 0.675 1.616 1.726 1.582 1.866 2.000
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74->id126807 MLDOSE 0.667 1.612 1.731 1.589 1.864 2.000
-75->id99016 MLDOSE 0.667 1.612 1.734 1.59 1.864 2.000
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76->id883847 MLDOSE 0.666 1.611 1.736 1.587 1.869 2.000
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78->id737255 MLDOSE 0.666 1.623 1.733 1.569 1.867 2.000
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93->id800145 MLDOSE 0.681 1.621 1.737 1.587 1.869 2.000
-94->id153857 MLDOSE 0.661 1.617 1.739 1.585 1.87 2.000
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99->id955526 MLDOSE 0.663 1.621 1.737 1.566 1.869 2.000
-100->id181850 MLDOSE 0.66 1.603 1.736 1.586 1.869 2.000
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101->id159506 MLDOSE 0.667 1.621 1.735 1.585 1.868 2.000
-102->id609051 MLDOSE 0.675 1.618 1.73 1.59 1.86 2.000
-103->id963886 MLDOSE 0.663 1.612 1.739 1.581 1.87 2.000
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104->id405792 MLDOSE 0.682 1.621 1.737 1.589 1.869 2.000
-105->id494172 MLDOSE 0.66 1.607 1.736 1.58 1.868 2.000
-106->id964637 MLDOSE 0.663 1.616 1.73 1.59 1.861 2.000
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111->id827034 MLDOSE 0.664 1.613 1.737 1.579 1.869 2.000
-112->id689645 MLDOSE 0.657 1.611 1.736 1.59 1.868 2.000
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113->id281585 MLDOSE 0.673 1.621 1.736 1.584 1.869 2.000
114->id885624 MLDOSE 0.672 1.619 1.734 1.585 1.869 2.000
-115->id577871 MLDOSE 0.67 1.616 1.731 1.585 1.864 2.000
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-121->id512328 MLDOSE 0.67 1.616 1.737 1.584 1.869 2.000
-122->id703534 MLDOSE 0.67 1.615 1.731 1.59 1.862 2.000
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124->id577169 MLDOSE 0.669 1.616 1.734 1.582 1.867 2.000
-125->id813971 MLDOSE 0.657 1.606 1.72 1.591 1.85 2.000
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128->id611178 MLDOSE 0.666 1.611 1.735 1.582 1.866 2.000
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-131->id435876 MLDOSE 0.678 1.619 1.739 1.586 1.87 2.000
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155->id711012 MLDOSE 0.672 1.605 1.736 1.575 1.868 2.000
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157->id789575 MLDOSE 0.658 1.618 1.733 1.591 1.863 2.000
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166->id223901 MLDOSE 0.666 1.615 1.733 1.576 1.868 2.000
167->id41320 MLDOSE 0.661 1.617 1.732 1.576 1.869 2.000
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-177->id41961 MLDOSE 0.66 1.62 1.737 1.572 1.867 2.000
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178->id257209 MLDOSE 0.673 1.616 1.736 1.588 1.869 2.000
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180->id957918 MLDOSE 0.663 1.618 1.726 1.581 1.869 2.000
-181->id975370 MLDOSE 0.67 1.614 1.738 1.583 1.87 2.000
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182->id889896 MLDOSE 0.679 1.618 1.733 1.589 1.869 2.000
-183->id978164 MLDOSE 0.669 1.62 1.735 1.586 1.868 2.000
-184->id90359 MLDOSE 0.675 1.621 1.737 1.58 1.869 2.000
-185->id307158 MLDOSE 0.675 1.615 1.71 1.591 1.86 2.000
+183->id978164 MLDOSE 0.669 1.620 1.735 1.586 1.868 2.000
+184->id90359 MLDOSE 0.675 1.621 1.737 1.580 1.869 2.000
+185->id307158 MLDOSE 0.675 1.615 1.710 1.591 1.860 2.000
186->id755940 MLDOSE 0.669 1.618 1.734 1.577 1.869 2.000
187->id995582 MLDOSE 0.666 1.615 1.724 1.591 1.853 2.000
188->id363965 MLDOSE 0.663 1.619 1.736 1.574 1.868 2.000
-189->id729124 MLDOSE 0.666 1.611 1.73 1.587 1.86 2.000
-190->id871963 MLDOSE 0.67 1.62 1.737 1.585 1.868 2.000
+189->id729124 MLDOSE 0.666 1.611 1.730 1.587 1.860 2.000
+190->id871963 MLDOSE 0.670 1.620 1.737 1.585 1.868 2.000
191->id475172 MLDOSE 0.663 1.621 1.737 1.579 1.869 2.000
192->id804699 MLDOSE 0.663 1.619 1.731 1.581 1.868 2.000
-193->id625843 MLDOSE 0.667 1.622 1.738 1.583 1.87 2.000
+193->id625843 MLDOSE 0.667 1.622 1.738 1.583 1.870 2.000
194->id595713 MLDOSE 0.657 1.599 1.736 1.588 1.869 2.000
195->id462604 MLDOSE 0.663 1.616 1.731 1.584 1.867 2.000
196->id106141 MLDOSE 0.672 1.612 1.732 1.589 1.864 2.000
197->id689349 MLDOSE 0.666 1.609 1.738 1.583 1.869 2.000
-198->id639003 MLDOSE 0.672 1.618 1.728 1.58 1.863 2.000
-199->id393896 MLDOSE 0.663 1.617 1.73 1.579 1.868 2.000
-200->id450307 MLDOSE 0.663 1.622 1.739 1.588 1.87 2.000
+198->id639003 MLDOSE 0.672 1.618 1.728 1.580 1.863 2.000
+199->id393896 MLDOSE 0.663 1.617 1.730 1.579 1.868 2.000
+200->id450307 MLDOSE 0.663 1.622 1.739 1.588 1.870 2.000
Modified: branches/ProbABEL-pvals/ProbABEL/checks/test_mms.sh
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/test_mms.sh 2014-12-29 14:01:35 UTC (rev 1901)
+++ branches/ProbABEL-pvals/ProbABEL/checks/test_mms.sh 2014-12-29 21:43:04 UTC (rev 1902)
@@ -1,6 +1,7 @@
#!/bin/bash
# This script runs checks on ProbABEL's palinear module for
# quantitative traits combined with the mmscore option.
+
echo "Analysis using MMScore..."
scriptdir=$(dirname $0)
@@ -26,6 +27,7 @@
exec 3>&1
fi
+echo "base analysis"
$palinear \
-p ${inputdir}/mmscore_pheno.PHE \
-i ${inputdir}/mmscore_gen.mlinfo \
@@ -34,7 +36,6 @@
-o mmscore_dose \
--mmscore ${inputdir}/mmscore_InvSigma_aj.sex.age.dat \
>& 3
-
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1902
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