[Genabel-commits] r997 - in pkg/ProbABEL: src tests tests/verified_results
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Nov 3 15:07:48 CET 2012
Author: lckarssen
Date: 2012-11-03 15:07:48 +0100 (Sat, 03 Nov 2012)
New Revision: 997
Added:
pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt
Removed:
pkg/ProbABEL/tests/verified_results/height_2df.out.txt
Modified:
pkg/ProbABEL/src/probabel.pl
pkg/ProbABEL/tests/Makefile.am
pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
Log:
ProbABEL:
- Improved checks of probabel.pl with output of probabilities
- probabel.pl now checks whether the option list passed on the command line contains the -o option. Instead of renaming the whole output (which went wrong with the chunked files) it now considers the argument to -o as part of the output file name.
- Cleaned up the chunk test script by using functions.
Modified: pkg/ProbABEL/src/probabel.pl
===================================================================
--- pkg/ProbABEL/src/probabel.pl 2012-11-01 21:38:51 UTC (rev 996)
+++ pkg/ProbABEL/src/probabel.pl 2012-11-03 14:07:48 UTC (rev 997)
@@ -19,7 +19,6 @@
my $_recess_file_postfix = "_recess.out.txt";
my $_over_domin_file_postfix = "_over_domin.out.txt";
-
# Separators in the config file
my $separator_cfg = ",";
my $chr_replacement = "_._chr_._";
@@ -28,8 +27,8 @@
# Set file locations
my $base_path = "./";
my @anprog = ($base_path . "palinear",
- $base_path . "palogist",
- $base_path . "pacoxph");
+ $base_path . "palogist",
+ $base_path . "pacoxph");
my $config = "probabel_config.cfg";
# Define the regression methods that are implemented
@@ -159,21 +158,34 @@
my $phename = $ARGV[5];
+my $outfile_prefix = $phename;
my $keys="";
for (my $i=6; $i<@ARGV; $i++) {
- $keys = $keys.$ARGV[$i]." ";
+ if ($ARGV[$i] eq "-o")
+ {
+ # Apparently the user wants to change the output file name
+ # Let's interpret this as an addition to our own prefix
+ $outfile_prefix = $outfile_prefix.$ARGV[$i+1];
+
+ # Skip the next argument (supposedly the addition to the
+ # output file name).
+ $i++;
+ }
+ else
+ {
+ $keys = $keys.$ARGV[$i]." ";
+ }
}
chop($keys);
-
-my $model_option_num=0;
+my $model_option_num = 0;
my $mldose_prob;
if($model eq "--additive") {
$mldose_prob = $mldose;
- $model_option_num=1;
+ $model_option_num = 1;
} elsif($model eq "--allmodels") {
$mldose_prob = $mlprob;
- $model_option_num=2;
+ $model_option_num = 2;
} else {
die "error: Wrong key for model. You can use \"--additive\" or \"--allmodels\" only\n";
}
@@ -208,7 +220,7 @@
my $head="--no-head";
}
- system "$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_arg -d $mldose_arg -m $legend_arg --chrom $chr -o $phename $head $keys";
+ system "$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_arg -d $mldose_arg -m $legend_arg --chrom $chr -o $outfile_prefix $head $keys";
exit;
}
@@ -245,53 +257,53 @@
$legend_arg =~ s/$chr_replacement/$chr/g;
$legend_arg =~ s/$chunk_replacement/$chunk/g;
- system "$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_arg -d $mldose_arg -m $legend_arg --chrom $chr -o $phename.chunk$chunk.chr$chr $head $keys";
+ system "$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_arg -d $mldose_arg -m $legend_arg --chrom $chr -o $outfile_prefix.chunk$chunk.chr$chr $head $keys";
if($model_option_num==2)
{
- `cat $phename.chunk${chunk}.chr${chr}$_2df_file_postfix >> ${phename}.${chr}${_2df_file_postfix}`;
- `rm $phename.chunk${chunk}.chr${chr}$_2df_file_postfix`;
+ `cat $outfile_prefix.chunk${chunk}.chr${chr}$_2df_file_postfix >> ${outfile_prefix}.${chr}${_2df_file_postfix}`;
+ `rm $outfile_prefix.chunk${chunk}.chr${chr}$_2df_file_postfix`;
- `cat $phename.chunk${chunk}.chr${chr}$_add_file_postfix >> ${phename}.${chr}${_add_file_postfix}`;
- `rm $phename.chunk${chunk}.chr${chr}$_add_file_postfix`;
+ `cat $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix >> ${outfile_prefix}.${chr}${_add_file_postfix}`;
+ `rm $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix`;
- `cat $phename.chunk${chunk}.chr${chr}$_domin_file_postfix >> ${phename}.${chr}${_domin_file_postfix}`;
- `rm $phename.chunk${chunk}.chr${chr}$_domin_file_postfix`;
+ `cat $outfile_prefix.chunk${chunk}.chr${chr}$_domin_file_postfix >> ${outfile_prefix}.${chr}${_domin_file_postfix}`;
+ `rm $outfile_prefix.chunk${chunk}.chr${chr}$_domin_file_postfix`;
- `cat $phename.chunk${chunk}.chr${chr}$_recess_file_postfix >> ${phename}.${chr}${_recess_file_postfix}`;
- `rm $phename.chunk${chunk}.chr${chr}$_recess_file_postfix`;
+ `cat $outfile_prefix.chunk${chunk}.chr${chr}$_recess_file_postfix >> ${outfile_prefix}.${chr}${_recess_file_postfix}`;
+ `rm $outfile_prefix.chunk${chunk}.chr${chr}$_recess_file_postfix`;
- `cat $phename.chunk${chunk}.chr${chr}$_over_domin_file_postfix >> ${phename}.${chr}${_over_domin_file_postfix}`;
- `rm $phename.chunk${chunk}.chr${chr}$_over_domin_file_postfix`;
+ `cat $outfile_prefix.chunk${chunk}.chr${chr}$_over_domin_file_postfix >> ${outfile_prefix}.${chr}${_over_domin_file_postfix}`;
+ `rm $outfile_prefix.chunk${chunk}.chr${chr}$_over_domin_file_postfix`;
} else {
- `cat $phename.chunk${chunk}.chr${chr}$_add_file_postfix >> $phename.${chr}${_add_file_postfix}`;
- print "cat $phename.chunk${chunk}.chr${chr}$_add_file_postfix >> $phename.chr${chr}${_add_file_postfix}\n";
- `rm $phename.chunk${chunk}.chr${chr}$_add_file_postfix`;
- print "rm $phename.chunk${chunk}.chr${chr}$_add_file_postfix\n";
+ `cat $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix >> $outfile_prefix.${chr}${_add_file_postfix}`;
+ print "cat $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix >> $outfile_prefix.chr${chr}${_add_file_postfix}\n";
+ `rm $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix`;
+ print "rm $outfile_prefix.chunk${chunk}.chr${chr}$_add_file_postfix\n";
}
}
if($model_option_num==2)
{
- `cat $phename.${chr}$_2df_file_postfix >> ${phename}${_2df_file_postfix}`;
- `rm $phename.${chr}$_2df_file_postfix`;
+ `cat $outfile_prefix.${chr}$_2df_file_postfix >> ${outfile_prefix}${_2df_file_postfix}`;
+ `rm $outfile_prefix.${chr}$_2df_file_postfix`;
- `cat $phename.${chr}$_add_file_postfix >> ${phename}${_add_file_postfix}`;
- `rm $phename.${chr}$_add_file_postfix`;
+ `cat $outfile_prefix.${chr}$_add_file_postfix >> ${outfile_prefix}${_add_file_postfix}`;
+ `rm $outfile_prefix.${chr}$_add_file_postfix`;
- `cat $phename.${chr}$_domin_file_postfix >> ${phename}${_domin_file_postfix}`;
- `rm $phename.${chr}$_domin_file_postfix`;
+ `cat $outfile_prefix.${chr}$_domin_file_postfix >> ${outfile_prefix}${_domin_file_postfix}`;
+ `rm $outfile_prefix.${chr}$_domin_file_postfix`;
- `cat $phename.${chr}$_recess_file_postfix >> ${phename}${_recess_file_postfix}`;
- `rm $phename.${chr}$_recess_file_postfix`;
+ `cat $outfile_prefix.${chr}$_recess_file_postfix >> ${outfile_prefix}${_recess_file_postfix}`;
+ `rm $outfile_prefix.${chr}$_recess_file_postfix`;
- `cat $phename.${chr}$_over_domin_file_postfix >> ${phename}${_over_domin_file_postfix}`;
- `rm $phename.${chr}$_over_domin_file_postfix`;
+ `cat $outfile_prefix.${chr}$_over_domin_file_postfix >> ${outfile_prefix}${_over_domin_file_postfix}`;
+ `rm $outfile_prefix.${chr}$_over_domin_file_postfix`;
} else {
- `cat $phename.${chr}$_add_file_postfix >> $phename${_add_file_postfix}`;
- print "cat $phename.${chr}$_add_file_postfix >> $phename${_add_file_postfix}\n";
- `rm $phename.${chr}$_add_file_postfix`;
- print "rm $phename.${chr}$_add_file_postfix\n";
+ `cat $outfile_prefix.${chr}$_add_file_postfix >> $outfile_prefix${_add_file_postfix}`;
+ print "cat $outfile_prefix.${chr}$_add_file_postfix >> $outfile_prefix${_add_file_postfix}\n";
+ `rm $outfile_prefix.${chr}$_add_file_postfix`;
+ print "rm $outfile_prefix.${chr}$_add_file_postfix\n";
}
}
Modified: pkg/ProbABEL/tests/Makefile.am
===================================================================
--- pkg/ProbABEL/tests/Makefile.am 2012-11-01 21:38:51 UTC (rev 996)
+++ pkg/ProbABEL/tests/Makefile.am 2012-11-03 14:07:48 UTC (rev 997)
@@ -4,17 +4,30 @@
tests_files = check_probabel.pl_chunk.sh
verified_results = verified_results/height_add.out.txt \
- verified_results/height_2df.out.txt
+ verified_results/height_ngp2_add.out.txt \
+ verified_results/height_ngp2_2df.out.txt \
+ verified_results/height_ngp2_domin.out.txt \
+ verified_results/height_ngp2_over_domin.out.txt \
+ verified_results/height_ngp2_recess.out.txt
+
dose_files = chr1.chunk1.dose chr1.chunk2.dose chr2.chunk1.dose \
chr2.chunk2.dose chr1.dose chr2.dose
+
prob_files = chr1.chunk1.prob chr1.chunk2.prob chr2.chunk1.prob \
chr2.chunk2.prob chr1.prob chr2.prob
+
map_files = chr1.chunk1.map chr1.chunk2.map chr2.chunk1.map \
chr2.chunk2.map chr1.map chr2.map
+
info_files = chr1.chunk1.info chr1.chunk2.info chr2.chunk1.info \
chr2.chunk2.info chr1.info chr2.info
+
output_files = height_add.out.txt height_2df.out.txt \
- height_domin.out.txt height_over_domin.out.txt height_recess.out.txt
+ height_domin.out.txt height_over_domin.out.txt height_recess.out.txt \
+ height_ngp2_recess.out.txt height_ngp2_domin.out.txt \
+ height_ngp2_over_domin.out.txt height_ngp2_2df.out.txt \
+ height_ngp2_add.out.txt
+
other_files = probabel.pl probabel_config.cfg height.PHE
Modified: pkg/ProbABEL/tests/check_probabel.pl_chunk.sh
===================================================================
--- pkg/ProbABEL/tests/check_probabel.pl_chunk.sh 2012-11-01 21:38:51 UTC (rev 996)
+++ pkg/ProbABEL/tests/check_probabel.pl_chunk.sh 2012-11-03 14:07:48 UTC (rev 997)
@@ -5,6 +5,7 @@
echo "Testing probabel.pl..."
+# -------- Set some default paths and file names -------
if [ -z ${srcdir} ]; then
srcdir="."
fi
@@ -39,80 +40,107 @@
>> probabel_config.cfg
-# ------------------ No chunks test -------------------
-# Split the dose, prob and info files up into two chromosomes with some
-# chunks
-awk '{print $1,$2,$3,$4}' $dosefile > chr1.dose
-awk '{print $1,$2,$5,$6,$7}' $dosefile > chr2.dose
+# ---------- function definitions ----------
+function prepare_input
+{
+ if [ "$1" == "nochunk" ]; then
+ # ------------------ No chunks test -------------------
+ # Split the dose, prob and info files up into two chromosomes
+ # with some chunks
+ awk '{print $1,$2,$3,$4}' $dosefile > chr1.dose
+ awk '{print $1,$2,$5,$6,$7}' $dosefile > chr2.dose
-awk '{print $1,$2,$3,$4,$5,$6}' $probfile > chr1.prob
-awk '{print $1,$2,$7,$8,$9,$10,$11,$12}' $probfile > chr2.prob
+ awk '{print $1,$2,$3,$4,$5,$6}' $probfile > chr1.prob
+ awk '{print $1,$2,$7,$8,$9,$10,$11,$12}' $probfile > chr2.prob
-sed -n '1,3p' $infofile > chr1.info
-sed -n '1p' $infofile > chr2.info
-sed -n '4,6p' $infofile >> chr2.info
+ sed -n '1,3p' $infofile > chr1.info
+ sed -n '1p' $infofile > chr2.info
+ sed -n '4,6p' $infofile >> chr2.info
-sed -n '1,3p' $mapfile > chr1.map
-sed -n '1p' $mapfile > chr2.map
-sed -n '4,6p' $mapfile >> chr2.map
+ sed -n '1,3p' $mapfile > chr1.map
+ sed -n '1p' $mapfile > chr2.map
+ sed -n '4,6p' $mapfile >> chr2.map
-# Run an analysis on dosage data
-outfile="height_add.out.txt"
-rm -f $outfile
-./probabel.pl 1 2 linear TestCohortNoChunk --additive height
-echo "Checking output using dosages without chunks..."
-diff $outfile $results/$outfile
+ WithOrWithout="without"
+ elif [ "$1" == "chunk" ]; then
+ # ------------------ Chunks test ----------------------
+ # Split the dose and info files up into two chromosomes with
+ # some chunks
+ awk '{print $1,$2,$3}' $dosefile > chr1.chunk1.dose
+ awk '{print $1,$2,$4}' $dosefile > chr1.chunk2.dose
+ awk '{print $1,$2,$5,$6}' $dosefile > chr2.chunk1.dose
+ awk '{print $1,$2,$7}' $dosefile > chr2.chunk2.dose
+ awk '{print $1,$2,$3,$4}' $probfile > chr1.chunk1.prob
+ awk '{print $1,$2,$5,$6}' $probfile > chr1.chunk2.prob
+ awk '{print $1,$2,$7,$8,$9,$10}' $probfile > chr2.chunk1.prob
+ awk '{print $1,$2,$11,$12}' $probfile > chr2.chunk2.prob
-# Run an analysis on probabilities
-outfile="height_2df.out.txt"
-rm -f $outfile
-./probabel.pl 1 2 linear TestCohortNoChunk --allmodels height
-echo "Checking output using probabilities without chunks..."
-diff $outfile $results/$outfile
+ sed -n '1,2p' $infofile > chr1.chunk1.info
+ sed -n '1p' $infofile > chr1.chunk2.info
+ sed -n '3p' $infofile >> chr1.chunk2.info
+ sed -n '1p' $infofile > chr2.chunk1.info
+ sed -n '4,5p' $infofile >> chr2.chunk1.info
+ sed -n '1p' $infofile > chr2.chunk2.info
+ sed -n '6p' $infofile >> chr2.chunk2.info
+ sed -n '1,2p' $mapfile > chr1.chunk1.map
+ sed -n '1p' $mapfile > chr1.chunk2.map
+ sed -n '3p' $mapfile >> chr1.chunk2.map
+ sed -n '1p' $mapfile > chr2.chunk1.map
+ sed -n '4,5p' $mapfile >> chr2.chunk1.map
+ sed -n '1p' $mapfile > chr2.chunk2.map
+ sed -n '6p' $mapfile >> chr2.chunk2.map
+ WithOrWithout="with"
+ else
+ echo "Run this function with one of these arguments: 'chunk'
+ or 'nochunk'."
+ exit 1
+ fi
-# ------------------ Chunks test ----------------------
-# Split the dose and info files up into two chromosomes with some
-# chunks
-awk '{print $1,$2,$3}' $dosefile > chr1.chunk1.dose
-awk '{print $1,$2,$4}' $dosefile > chr1.chunk2.dose
-awk '{print $1,$2,$5,$6}' $dosefile > chr2.chunk1.dose
-awk '{print $1,$2,$7}' $dosefile > chr2.chunk2.dose
+}
-awk '{print $1,$2,$3,$4}' $probfile > chr1.chunk1.prob
-awk '{print $1,$2,$5,$6}' $probfile > chr1.chunk2.prob
-awk '{print $1,$2,$7,$8,$9,$10}' $probfile > chr2.chunk1.prob
-awk '{print $1,$2,$11,$12}' $probfile > chr2.chunk2.prob
-sed -n '1,2p' $infofile > chr1.chunk1.info
-sed -n '1p' $infofile > chr1.chunk2.info
-sed -n '3p' $infofile >> chr1.chunk2.info
-sed -n '1p' $infofile > chr2.chunk1.info
-sed -n '4,5p' $infofile >> chr2.chunk1.info
-sed -n '1p' $infofile > chr2.chunk2.info
-sed -n '6p' $infofile >> chr2.chunk2.info
+function run_test
+{
+ # Run an analysis on dosage data
+ outfile="height_add.out.txt"
+ rm -f $outfile
+ ./probabel.pl 1 2 linear TestCohortChunk --additive height
+ echo "Checking output using dosages $WithOrWithout chunks..."
+ diff $outfile $results/$outfile
-sed -n '1,2p' $mapfile > chr1.chunk1.map
-sed -n '1p' $mapfile > chr1.chunk2.map
-sed -n '3p' $mapfile >> chr1.chunk2.map
-sed -n '1p' $mapfile > chr2.chunk1.map
-sed -n '4,5p' $mapfile >> chr2.chunk1.map
-sed -n '1p' $mapfile > chr2.chunk2.map
-sed -n '6p' $mapfile >> chr2.chunk2.map
+ # Run an analysis on probabilities
+ outfilelist[1]="height_ngp2_2df.out.txt"
+ outfilelist[2]="height_ngp2_recess.out.txt"
+ outfilelist[3]="height_ngp2_over_domin.out.txt"
+ outfilelist[4]="height_ngp2_domin.out.txt"
+ outfilelist[5]="height_ngp2_add.out.txt"
+ for i in {1..5}; do
+ rm -f ${outfilelist[$i]}
+ done
-# Run an analysis on dosage data
-outfile="height_add.out.txt"
-rm -f $outfile
-./probabel.pl 1 2 linear TestCohortChunk --additive height
-echo "Checking output using dosages with chunks..."
-diff $outfile $results/$outfile
+ ./probabel.pl 1 2 linear TestCohortNoChunk --allmodels height -o _ngp2
+ echo "Checking output using probabilities $WithOrWithout chunks..."
+ for i in {1..5}; do
+ echo -n " Verifying ${outfilelist[$i]}"
+ diff ${outfilelist[$i]} $results/${outfilelist[$i]}
+ if [ $? == 0 ]; then
+ echo -e "\t\tOK"
+ else
+ echo -e "\t\tFAILED"
+ fi
+ done
+}
+# ---------- Continuation of the main function ----------
+prepare_input nochunk
-# Run an analysis on probabilities
-outfile="height_2df.out.txt"
-rm -f $outfile
-./probabel.pl 1 2 linear TestCohortNoChunk --allmodels height
-echo "Checking output using probabilities without chunks:"
-diff $outfile $results/$outfile
+run_test
+echo "-------------------- Finished check without chunks --------------------"
+
+prepare_input chunk
+
+run_test
+echo "-------------------- Finished check with chunks --------------------"
Deleted: pkg/ProbABEL/tests/verified_results/height_2df.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_2df.out.txt 2012-11-01 21:38:51 UTC (rev 996)
+++ pkg/ProbABEL/tests/verified_results/height_2df.out.txt 2012-11-03 14:07:48 UTC (rev 997)
@@ -1,6 +0,0 @@
-name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_A1A2 beta_SNP_A1A1 sebeta_SNP_A1A2 sebeta_SNP_A1A1 loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 615.049 1057.49 -539.487 1040.54 -428.817
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -820.352 1392.51 -646.025 1054.18 -426.797
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -239.797 1308.51 -246.735 1102.06 -428.924
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 782.576 1474.59 604.391 1064.24 -428.789
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 1180.53 1104.39 912.574 1003.85 -427.981
Added: pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt (rev 0)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt 2012-11-03 14:07:48 UTC (rev 997)
@@ -0,0 +1,6 @@
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_A1A2 beta_SNP_A1A1 sebeta_SNP_A1A2 sebeta_SNP_A1A1 loglik
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 615.049 1057.49 -539.487 1040.54 -428.817
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -820.352 1392.51 -646.025 1054.18 -426.797
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -239.797 1308.51 -246.735 1102.06 -428.924
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 782.576 1474.59 604.391 1064.24 -428.789
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 1180.53 1104.39 912.574 1003.85 -427.981
Added: pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt (rev 0)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt 2012-11-03 14:07:48 UTC (rev 997)
@@ -0,0 +1,6 @@
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_addA1 sebeta_SNP_addA1 loglik
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 20.3848 76.6301 -428.98
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -25.7626 86.4878 -426.965
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -40.7723 102.559 -428.936
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 35.361 81.7867 -428.921
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 -112.234 141.168 -428.694
Added: pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt (rev 0)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt 2012-11-03 14:07:48 UTC (rev 997)
@@ -0,0 +1,6 @@
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_domA1 sebeta_SNP_domA1 loglik
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 33.0595 115.333 -428.974
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -178.128 417.233 -426.917
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -272.156 640.297 -428.924
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 188.396 361.092 -428.877
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 285.007 898.508 -428.965
Added: pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt (rev 0)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt 2012-11-03 14:07:48 UTC (rev 997)
@@ -0,0 +1,6 @@
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_odom sebeta_SNP_odom loglik
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 80.0816 231.105 -428.955
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 28.4979 142.757 -426.989
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 51.4168 142.042 -428.95
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 -50.7539 145.509 -428.954
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 188.854 172.317 -428.404
Added: pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt (rev 0)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt 2012-11-03 14:07:48 UTC (rev 997)
@@ -0,0 +1,6 @@
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_recA1 sebeta_SNP_recA1 loglik
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 51.0128 227.445 -428.991
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -28.2735 108.063 -426.975
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -45.9706 119.627 -428.941
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 42.3583 105.005 -428.933
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 -147.318 156.768 -428.566
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