[Genabel-commits] r1489 - in branches/ProbABEL-pvals/ProbABEL: checks doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Dec 19 22:53:57 CET 2013
Author: lckarssen
Date: 2013-12-19 22:53:57 +0100 (Thu, 19 Dec 2013)
New Revision: 1489
Added:
branches/ProbABEL-pvals/ProbABEL/doc/probabel.pl.1
Modified:
branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am
branches/ProbABEL-pvals/ProbABEL/checks/test_qt.sh
branches/ProbABEL-pvals/ProbABEL/doc/Makefile.am
branches/ProbABEL-pvals/ProbABEL/doc/ProbABEL_manual.tex
branches/ProbABEL-pvals/ProbABEL/src/Makefile.am
branches/ProbABEL-pvals/ProbABEL/src/probabel.pl
Log:
Merging trunk r1449 through r1488 into this branch.
Modified: branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am 2013-12-19 21:27:44 UTC (rev 1488)
+++ branches/ProbABEL-pvals/ProbABEL/checks/Makefile.am 2013-12-19 21:53:57 UTC (rev 1489)
@@ -56,9 +56,7 @@
TESTS = $(check_SCRIPTS)
-testsdir = $(pkgdatadir)/tests
-dist_tests_DATA = $(verified_results) $(input_files)
-dist_tests_SCRIPTS = $(check_SCRIPTS)
+EXTRA_DIST = $(verified_results) $(input_files) $(check_SCRIPTS)
##################################################
@@ -72,46 +70,46 @@
logist_prob_domin.out.txt logist_prob_fv_recess.out.txt \
logist_prob_fv_over_domin.out.txt logist_prob_recess.out.txt
-cleanfiles_qt = height_base_add.out.txt height_base_fv_add.out.txt \
-height_allcov_add.out.txt height_allcov_fv_add.out.txt \
-height_int1_add.out.txt height_int1_fv_add.out.txt \
-height_robust_add.out.txt height_robust_fv_add.out.txt \
-height_robust_int1_add.out.txt height_robust_int1_fv_add.out.txt \
-height_ngp2_add.out.txt height_ngp2_fv_add.out.txt \
-height_ngp2_domin.out.txt height_ngp2_fv_domin.out.txt \
-height_ngp2_over_domin.out.txt height_ngp2_fv_over_domin.out.txt \
-height_ngp2_recess.out.txt height_ngp2_fv_recess.out.txt \
-height_ngp2_2df.out.txt height_ngp2_fv_2df.out.txt \
-height_ngp2_allcov_add.out.txt height_ngp2_allcov_fv_add.out.txt \
-height_ngp2_allcov_domin.out.txt height_ngp2_allcov_fv_domin.out.txt \
-height_ngp2_allcov_over_domin.out.txt \
-height_ngp2_allcov_fv_over_domin.out.txt \
-height_ngp2_allcov_recess.out.txt height_ngp2_allcov_fv_recess.out.txt \
-height_ngp2_allcov_recess.out.txt height_ngp2_allcov_fv_recess.out.txt \
-height_ngp2_int1_add.out.txt height_ngp2_int1_fv_add.out.txt \
-height_ngp2_int1_domin.out.txt height_ngp2_int1_fv_domin.out.txt \
-height_ngp2_int1_over_domin.out.txt \
-height_ngp2_int1_fv_over_domin.out.txt height_ngp2_int1_recess.out.txt \
-height_ngp2_int1_fv_recess.out.txt height_ngp2_int1_2df.out.txt \
-height_ngp2_int1_fv_2df.out.txt height_ngp2_robust_add.out.txt \
-height_ngp2_robust_fv_add.out.txt height_ngp2_robust_domin.out.txt \
-height_ngp2_robust_fv_domin.out.txt \
-height_ngp2_robust_over_domin.out.txt \
-height_ngp2_robust_fv_over_domin.out.txt \
-height_ngp2_robust_recess.out.txt height_ngp2_robust_fv_recess.out.txt \
-height_ngp2_robust_2df.out.txt height_ngp2_robust_fv_2df.out.txt \
-height_ngp2_robust_int1_add.out.txt \
-height_ngp2_robust_int1_fv_add.out.txt \
-height_ngp2_robust_int1_domin.out.txt \
-height_ngp2_robust_int1_fv_domin.out.txt \
-height_ngp2_robust_int1_over_domin.out.txt \
-height_ngp2_robust_int1_fv_over_domin.out.txt \
-height_ngp2_robust_int1_recess.out.txt \
-height_ngp2_robust_int1_fv_recess.out.txt \
-height_ngp2_robust_int1_2df.out.txt \
-height_ngp2_robust_int1_fv_2df.out.txt \
-height_ngp2_allcov_fv_2df.out.txt height_ngp2_robust_fv_add.out.txt \
-height_ngp2_allcov_2df.out.txt
+cleanfiles_qt = linear_base_add.out.txt linear_base_fv_add.out.txt \
+linear_allcov_add.out.txt linear_allcov_fv_add.out.txt \
+linear_int1_add.out.txt linear_int1_fv_add.out.txt \
+linear_robust_add.out.txt linear_robust_fv_add.out.txt \
+linear_robust_int1_add.out.txt linear_robust_int1_fv_add.out.txt \
+linear_ngp2_add.out.txt linear_ngp2_fv_add.out.txt \
+linear_ngp2_domin.out.txt linear_ngp2_fv_domin.out.txt \
+linear_ngp2_over_domin.out.txt linear_ngp2_fv_over_domin.out.txt \
+linear_ngp2_recess.out.txt linear_ngp2_fv_recess.out.txt \
+linear_ngp2_2df.out.txt linear_ngp2_fv_2df.out.txt \
+linear_ngp2_allcov_add.out.txt linear_ngp2_allcov_fv_add.out.txt \
+linear_ngp2_allcov_domin.out.txt linear_ngp2_allcov_fv_domin.out.txt \
+linear_ngp2_allcov_over_domin.out.txt \
+linear_ngp2_allcov_fv_over_domin.out.txt \
+linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
+linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
+linear_ngp2_int1_add.out.txt linear_ngp2_int1_fv_add.out.txt \
+linear_ngp2_int1_domin.out.txt linear_ngp2_int1_fv_domin.out.txt \
+linear_ngp2_int1_over_domin.out.txt \
+linear_ngp2_int1_fv_over_domin.out.txt linear_ngp2_int1_recess.out.txt \
+linear_ngp2_int1_fv_recess.out.txt linear_ngp2_int1_2df.out.txt \
+linear_ngp2_int1_fv_2df.out.txt linear_ngp2_robust_add.out.txt \
+linear_ngp2_robust_fv_add.out.txt linear_ngp2_robust_domin.out.txt \
+linear_ngp2_robust_fv_domin.out.txt \
+linear_ngp2_robust_over_domin.out.txt \
+linear_ngp2_robust_fv_over_domin.out.txt \
+linear_ngp2_robust_recess.out.txt linear_ngp2_robust_fv_recess.out.txt \
+linear_ngp2_robust_2df.out.txt linear_ngp2_robust_fv_2df.out.txt \
+linear_ngp2_robust_int1_add.out.txt \
+linear_ngp2_robust_int1_fv_add.out.txt \
+linear_ngp2_robust_int1_domin.out.txt \
+linear_ngp2_robust_int1_fv_domin.out.txt \
+linear_ngp2_robust_int1_over_domin.out.txt \
+linear_ngp2_robust_int1_fv_over_domin.out.txt \
+linear_ngp2_robust_int1_recess.out.txt \
+linear_ngp2_robust_int1_fv_recess.out.txt \
+linear_ngp2_robust_int1_2df.out.txt \
+linear_ngp2_robust_int1_fv_2df.out.txt \
+linear_ngp2_allcov_fv_2df.out.txt linear_ngp2_robust_fv_add.out.txt \
+linear_ngp2_allcov_2df.out.txt
cleanfiles_mms = mmscore_dose_add.out.txt mmscore_dose_fv_add.out.txt \
mmscore_prob_fv_over_domin.out.txt mmscore_prob_fv_domin.out.txt \
Modified: branches/ProbABEL-pvals/ProbABEL/checks/test_qt.sh
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/checks/test_qt.sh 2013-12-19 21:27:44 UTC (rev 1488)
+++ branches/ProbABEL-pvals/ProbABEL/checks/test_qt.sh 2013-12-19 21:53:57 UTC (rev 1489)
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -x
# This script runs checks on ProbABEL's palinear module for
# quantitative traits.
@@ -25,7 +25,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 \
- -o height_base \
+ -o linear_base \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -33,12 +33,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 \
- -o height_base_fv \
+ -o linear_base_fv \
>& 3
#echo -n "QT check: dose vs. dose_fv"
-run_diff height_base_add.out.txt \
- height_base_fv_add.out.txt \
+run_diff linear_base_add.out.txt \
+ linear_base_fv_add.out.txt \
"QT check: dose vs. dose_fv"
@@ -48,7 +48,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --allcov \
- -o height_allcov \
+ -o linear_allcov \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -56,11 +56,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --allcov \
- -o height_allcov_fv \
+ -o linear_allcov_fv \
>& 3
-run_diff height_allcov_add.out.txt \
- height_allcov_fv_add.out.txt \
+run_diff linear_allcov_add.out.txt \
+ linear_allcov_fv_add.out.txt \
"QT check: allcov: dose vs. dose_fv"
@@ -71,7 +71,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --interaction=1 \
- -o height_int1 \
+ -o linear_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -79,11 +79,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --interaction=1 \
- -o height_int1_fv \
+ -o linear_int1_fv \
>& 3
-run_diff height_int1_add.out.txt \
- height_int1_fv_add.out.txt \
+run_diff linear_int1_add.out.txt \
+ linear_int1_fv_add.out.txt \
"QT check: interactions: dose vs. dose_fv"
@@ -94,7 +94,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust \
- -o height_robust \
+ -o linear_robust \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -102,11 +102,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust \
- -o height_robust_fv \
+ -o linear_robust_fv \
>& 3
-run_diff height_robust_add.out.txt \
- height_robust_fv_add.out.txt \
+run_diff linear_robust_add.out.txt \
+ linear_robust_fv_add.out.txt \
"QT check: robust: dose vs. dose_fv"
@@ -117,7 +117,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust --interaction=1 \
- -o height_robust_int1 \
+ -o linear_robust_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -125,11 +125,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust --interaction=1 \
- -o height_robust_int1_fv \
+ -o linear_robust_int1_fv \
>& 3
-run_diff height_robust_int1_add.out.txt \
- height_robust_int1_fv_add.out.txt \
+run_diff linear_robust_int1_add.out.txt \
+ linear_robust_int1_fv_add.out.txt \
"QT check: robust & interaction: dose vs. dose_fv"
@@ -140,7 +140,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 \
- -o height_ngp2 \
+ -o linear_ngp2 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -148,18 +148,18 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 \
- -o height_ngp2_fv \
+ -o linear_ngp2_fv \
>& 3
# Remove header from the outputs, because they differ
-run_diff height_base_add.out.txt \
- height_ngp2_add.out.txt \
+run_diff linear_base_add.out.txt \
+ linear_ngp2_add.out.txt \
"QT check: dose vs. prob (additive model)" -I SNP
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_${model}.out.txt \
- height_ngp2_fv_${model}.out.txt \
+ run_diff linear_ngp2_${model}.out.txt \
+ linear_ngp2_fv_${model}.out.txt \
"QT check ($model model): prob vs. prob_fv"
done
@@ -171,7 +171,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --allcov \
- -o height_ngp2_allcov \
+ -o linear_ngp2_allcov \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -179,12 +179,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --allcov \
- -o height_ngp2_allcov_fv \
+ -o linear_ngp2_allcov_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_allcov_${model}.out.txt \
- height_ngp2_allcov_fv_${model}.out.txt \
+ run_diff linear_ngp2_allcov_${model}.out.txt \
+ linear_ngp2_allcov_fv_${model}.out.txt \
"QT check --allcov ($model model): prob vs. prob_fv"
done
@@ -196,7 +196,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --interaction=1 \
- -o height_ngp2_int1 \
+ -o linear_ngp2_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -204,12 +204,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --interaction=1 \
- -o height_ngp2_int1_fv \
+ -o linear_ngp2_int1_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_int1_${model}.out.txt \
- height_ngp2_int1_fv_${model}.out.txt \
+ run_diff linear_ngp2_int1_${model}.out.txt \
+ linear_ngp2_int1_fv_${model}.out.txt \
"QT check --interactions ($model model): prob vs. prob_fv"
done
@@ -221,7 +221,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust \
- -o height_ngp2_robust \
+ -o linear_ngp2_robust \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -229,12 +229,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust \
- -o height_ngp2_robust_fv \
+ -o linear_ngp2_robust_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_robust_${model}.out.txt \
- height_ngp2_robust_fv_${model}.out.txt \
+ run_diff linear_ngp2_robust_${model}.out.txt \
+ linear_ngp2_robust_fv_${model}.out.txt \
"QT check --robust ($model model): prob vs. prob_fv"
done
@@ -246,7 +246,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust --interaction=1 \
- -o height_ngp2_robust_int1 \
+ -o linear_ngp2_robust_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -254,11 +254,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust --interaction=1 \
- -o height_ngp2_robust_int1_fv \
+ -o linear_ngp2_robust_int1_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_robust_int1_${model}.out.txt \
- height_ngp2_robust_int1_fv_${model}.out.txt \
+ run_diff linear_ngp2_robust_int1_${model}.out.txt \
+ linear_ngp2_robust_int1_fv_${model}.out.txt \
"QT check --robust --interactions ($model model): prob vs. prob_fv"
done
Modified: branches/ProbABEL-pvals/ProbABEL/doc/Makefile.am
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/doc/Makefile.am 2013-12-19 21:27:44 UTC (rev 1488)
+++ branches/ProbABEL-pvals/ProbABEL/doc/Makefile.am 2013-12-19 21:53:57 UTC (rev 1489)
@@ -6,7 +6,7 @@
test.mlinfo test_regression.R COPYING LICENSE INSTALL ChangeLog \
TODO
-man_MANS =
+man_MANS = probabel.pl.1
if BUILD_palinear
man_MANS += palinear.1
endif
Modified: branches/ProbABEL-pvals/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/doc/ProbABEL_manual.tex 2013-12-19 21:27:44 UTC (rev 1488)
+++ branches/ProbABEL-pvals/ProbABEL/doc/ProbABEL_manual.tex 2013-12-19 21:53:57 UTC (rev 1489)
@@ -1,14 +1,15 @@
\documentclass[12pt,a4paper]{article}
\title{Manual for ProbABEL v0.4.2}
-\author{\emph{Current Programmers:} Lennart Karssen$^{1}$, Maarten
- Kooyman$^1$, \\
- Yurii Aulchenko$^{2}$ \\
+\author{\emph{Current Programmers:} Lennart Karssen$^{1,2}$, Maarten
+ Kooyman$^2$, \\
+ Yurii Aulchenko$^{1,3}$ \\
\emph{Former Programmers:} Maksim Struchalin
\\
\\
- $^{1}${\small Erasmus MC, Rotterdam} \\
- $^{2}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
+ $^{1}${\small YuriiA Consulting} \\
+ $^{2}${\small Erasmus MC, Rotterdam}\\
+ $^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
}
\date{\today}
Copied: branches/ProbABEL-pvals/ProbABEL/doc/probabel.pl.1 (from rev 1488, pkg/ProbABEL/doc/probabel.pl.1)
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/doc/probabel.pl.1 (rev 0)
+++ branches/ProbABEL-pvals/ProbABEL/doc/probabel.pl.1 2013-12-19 21:53:57 UTC (rev 1489)
@@ -0,0 +1,73 @@
+.TH probabel.pl 1 "12 December 2013"
+.SH NAME
+probabel.pl \- Wrapper around the three ProbABEL binaries, simplifying their use
+.SH SYNOPSIS
+.B probabel.pl
+.BI "" "CHROM-START CHROM-STOP METHOD COHORT MODEL PHENOTYPE [OTHER_OPTIONS]"
+.SH DESCRIPTION
+.B probabel.pl
+is a wrapper around the three ProbABEL binaries: \fBpalinear\fR,
+\fBpalogist\fR, and \fBpacoxph\fR.
+.PP
+It is designed to simplify runnig of a Genome-Wide Association Study
+(GWAS) by saving the user's precious time in two ways:
+.PP
+1) it runs the regression analysis of all chromosomes from \fICHROM-START\fR to
+\fICHROM-STOP\fR.
+.PP
+2) In contrast to the three binaries mentioned above,
+with \fBprobabel.pl\fR the user doesn't need to specify the locations
+of the required genetic data files. Their location is centrally
+managed in a configuration file (\fI/etc/probabel_config.cfg\fR by default).
+
+.SH OPTIONS
+.SS Required command line options
+.TP
+.I CHROM-START
+Number of the chromosome to start the analysis at.
+.TP
+.I CHROM-END
+Number of the chromosome to end the analysis at.
+.PP
+Note that analysis of a single chromosome can be run by specifying the
+same number for \fICHROM-START\fR and \fICHROM-STOP\fR. In fact, this
+is the way to run analysis for the X or Y chromosome
+.TP
+.I METHOD
+Which regression method to use, can be one of \fIlinear\fR,
+\fIlogistic,\fR or \fIcoxph\fR.
+
+.TP
+.I COHORT
+The name of the cohort as defined in the
+\fI/etc/probabel_config.cfg\fR file. Using the cohort identifier from
+the config file the three actual ProbABEL binaries know where to find
+the genotypic information files (dosage files and/or probability
+files).
+.TP
+.I MODEL
+The genetic model to be used. Can be either \fB--additive\fR for the
+additive model (requires genotype data in dosage form), or
+\fB--allmodels\fR to run all genetic models: additive, recessive,
+dominant, over-dominant and 2df.
+.TP
+.I PHENOTYPE
+The name of the phenotype file, without its extension (which should be
+\fI.PHE\fR!).
+
+.SS Other options
+Any options listed after the (mandatory) previous ones will be passed
+on to the underlying binary: \fBpalinear\fR, \fBpalogist\fR or
+\fBpacoxph\fR, depending on the \fIMETHOD\fR.
+.PP
+The most commonly used option is the \fB\-o\fR option, followed by a
+file name, this specifies the beginning of the file name for the
+output files.
+
+.SS Additional options
+.B "\-h, \-\-help"
+Get additional help on how to run \fBprobabel.pl\fR. In this case none of
+the other options needs to be specified.
+
+.SH EXAMPLES
+probabel.pl 1 22 linear "My_Large_Cohort" \-\-additive my_phenotype
Modified: branches/ProbABEL-pvals/ProbABEL/src/Makefile.am
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/src/Makefile.am 2013-12-19 21:27:44 UTC (rev 1488)
+++ branches/ProbABEL-pvals/ProbABEL/src/Makefile.am 2013-12-19 21:53:57 UTC (rev 1489)
@@ -80,11 +80,11 @@
extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
## Install these scripts in the bin directory as well:
-dist_bin_SCRIPTS = probabel.pl extIDS.pl
+dist_bin_SCRIPTS = probabel.pl
## Install this R script in the examples directory
scriptdir = $(pkgdatadir)/scripts
-dist_script_DATA = prepare_data.R
+dist_script_DATA = prepare_data.R extIDS.pl
## Install the config file
dist_sysconf_DATA = probabel_config.cfg.example
@@ -95,3 +95,7 @@
$(DESTDIR)$(bindir)/probabel.pl
$(SED) -i "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel.pl
$(SED) -i "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel.pl
+
+## Make the script executable
+install-data-hook:
+ chmod a+rx $(DESTDIR)/$(scriptdir)/extIDS.pl
Modified: branches/ProbABEL-pvals/ProbABEL/src/probabel.pl
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/src/probabel.pl 2013-12-19 21:27:44 UTC (rev 1488)
+++ branches/ProbABEL-pvals/ProbABEL/src/probabel.pl 2013-12-19 21:53:57 UTC (rev 1489)
@@ -103,7 +103,8 @@
probabel.pl 1 22 \"method\" \"cohort\" --model name_of_file
Change \"method\", \"cohort\" and --model to appropriate values\n";
print "\n Version: $version";
- print "\n\n Authors: Lennart Karssen - l.karssen\@erasmusmc.nl,
+ print "\n\n Authors: Lennart Karssen - lennart\@karssen.org,
+ Maarten Kooyman - m.kooijman\@erasmusmc.nl,
Maksim Struchalin - m.struchalin\@erasmusmc.nl,
Yurii Aulchenko - yurii.aulchenko\@gmail.com.\n\n";
}
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