From f7c1f074fc0c35981ae1a9db2df6b27c42c99655 Mon Sep 17 00:00:00 2001 From: dtaliun Date: Tue, 5 May 2020 09:03:26 -0400 Subject: [PATCH] Control float print precision --- metal/Main.cpp | 36 +- tests/CMakeLists.txt | 7 + tests/test_10/METAANALYSIS1.TBL | 2496 +++++++++++++++++++++++++++++++ tests/test_10/metal.txt | 68 + version/VersionInfo.h | 2 +- 5 files changed, 2599 insertions(+), 10 deletions(-) create mode 100644 tests/test_10/METAANALYSIS1.TBL create mode 100755 tests/test_10/metal.txt diff --git a/metal/Main.cpp b/metal/Main.cpp index fa5b2cd..7a00670 100644 --- a/metal/Main.cpp +++ b/metal/Main.cpp @@ -78,6 +78,8 @@ bool strictColumnCounting = true; bool verbose = false; bool logPValue = false; bool trackPositions = false; +int effectPrintPrecision = 4; +int stderrPrintPrecision = 4; String genomicControlFilter; double genomicControlLambda = 0.0; @@ -646,9 +648,9 @@ void Analyze(bool heterogeneity) { fprintf(f, "%.4f\t%.4f\t", minFrequency, maxFrequency); fprintf(f, "%.*f\t%.*f\t", - useStandardErrors ? 4 : 2, + useStandardErrors ? effectPrintPrecision : 2, useStandardErrors ? statistics[marker] / weights[marker] : weights[marker], - useStandardErrors ? 4 : 3, + useStandardErrors ? stderrPrintPrecision : 3, useStandardErrors ? sqrt(1.0 / weights[marker]) : statistic); if (studyOverlap) { @@ -1708,12 +1710,14 @@ void ShowHelp(bool startup) "# ZCUTOFF [NUMBER] (%s = %.1f)\n" "#\n" "# Options for general analysis control ...\n" - "# PROCESSFILE [FILENAME]\n" - "# OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL')\n" - "# MAXWARNINGS [NUMBER] (%s = %d)\n" - "# VERBOSE [ON|OFF] (%s = '%s')\n" - "# LOGPVALUE [ON|OFF] (%s = '%s')\n" - "# ANALYZE [HETEROGENEITY]\n" + "# PROCESSFILE [FILENAME]\n" + "# OUTFILE [PREFIX SUFFIX] (default = 'METAANALYSIS','.TBL')\n" + "# MAXWARNINGS [NUMBER] (%s = %d)\n" + "# VERBOSE [ON|OFF] (%s = '%s')\n" + "# LOGPVALUE [ON|OFF] (%s = '%s')\n" + "# EFFECT_PRINT_PRECISION [NUMBER] (%s = '%d')\n" + "# STDERR_PRINT_PRECISION [NUMBER] (%s = '%d')\n" + "# ANALYZE [HETEROGENEITY]\n" "# CLEAR\n\n" "# Options for general run control ...\n" "# SOURCE [SCRIPTFILE]\n" @@ -1742,7 +1746,9 @@ void ShowHelp(bool startup) setting, zCutoff, setting, maxWarnings, setting, verbose ? "ON" : "OFF", - setting, logPValue ? "ON" : "OFF"); + setting, logPValue ? "ON" : "OFF", + setting, effectPrintPrecision, + setting, stderrPrintPrecision); } void RunScript(FILE * file) @@ -2131,6 +2137,18 @@ void RunScript(FILE * file) } } + if ((tokens[0].MatchesBeginningOf("EFFECT_PRINT_PRECISION") == 0) && (tokens.Length() > 1)) { + effectPrintPrecision = tokens[1].AsInteger(); + printf("## Set print pecision for Effect to %d ...\n", effectPrintPrecision); + continue; + } + + if ((tokens[0].MatchesBeginningOf("STDERR_PRINT_PRECISION") == 0) && (tokens.Length() > 1)) { + stderrPrintPrecision = tokens[1].AsInteger(); + printf("## Set print pecision for StdErr to %d ...\n", stderrPrintPrecision); + continue; + } + if (tokens[0].MatchesBeginningOf("ZCUTOFF") == 0) { zCutoff = tokens[1].AsDouble(); printf("## Set Z cutoff to %.2f ...\n", zCutoff); diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index 6bef0f1..7991511 100644 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -75,4 +75,11 @@ add_test(NAME TRACK_POSITIONS WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/test COMMAND ${CMAKE_COMMAND} -DMETAL=${CMAKE_BINARY_DIR}/metal/metal -DMETAL_TBL=${CMAKE_CURRENT_SOURCE_DIR}/test_09/METAANALYSIS1.TBL + -P ${CMAKE_CURRENT_SOURCE_DIR}/compare.cmake) + +file(COPY test_10 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) +add_test(NAME PRINT_PRECISION WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/test_10 + COMMAND ${CMAKE_COMMAND} + -DMETAL=${CMAKE_BINARY_DIR}/metal/metal + -DMETAL_TBL=${CMAKE_CURRENT_SOURCE_DIR}/test_10/METAANALYSIS1.TBL -P ${CMAKE_CURRENT_SOURCE_DIR}/compare.cmake) \ No newline at end of file diff --git a/tests/test_10/METAANALYSIS1.TBL b/tests/test_10/METAANALYSIS1.TBL new file mode 100644 index 0000000..6d8dcdd --- /dev/null +++ b/tests/test_10/METAANALYSIS1.TBL @@ -0,0 +1,2496 @@ +MarkerName Allele1 Allele2 Effect StdErr P-value Direction +rs217377 t c 0.012201585874 0.014019751651 0.3841 +++ +rs4668077 a g -0.006188892135 0.017053019568 0.7167 --+ +rs16855496 a g -0.011000000000 0.118000000000 0.9257 ??- +rs217386 a g 0.009891639322 0.015388864091 0.5204 +0+ +rs2075070 a g -0.011315468871 0.012989147319 0.3837 --+ +rs10187002 a t 0.012000000000 0.122000000000 0.9216 ??+ +rs12785983 t c -0.010949965501 0.014436371525 0.4482 +-- +rs1100405 t c -0.017824494916 0.013201553946 0.177 +-- +rs12155014 t c 0.019442164179 0.021464934094 0.3651 ++- +rs2287619 t c -0.061851440635 0.025282507293 0.01443 --- +rs505899 a t -0.013605649625 0.017299911256 0.4316 +-- +rs4753424 t c 0.031029383634 0.014557346061 0.03305 +++ +rs2724155 a c 0.011017060721 0.023833824157 0.6439 +++ +rs6718042 a c 0.003217995578 0.030667013800 0.9164 --+ +rs3845732 t c 0.010277009637 0.019105541653 0.5906 +-+ +rs3755166 a g -0.007022468260 0.013036739637 0.5901 +-- +rs768919 c g 0.026636883476 0.037241231116 0.4745 +-+ +rs4753444 t c -0.003321952817 0.012980165201 0.798 --+ +rs2433681 a g -0.014938032489 0.022522007148 0.5072 -+- +rs13393173 a g 0.004996242525 0.014906382995 0.7375 -0+ +rs6433109 a c 0.019362409042 0.013105992913 0.1396 +++ +rs3019218 c g 0.004857121299 0.012874431347 0.706 -++ +rs512498 t c 0.000545020792 0.013018745048 0.9666 ++- +rs2595650 a g -0.003329374790 0.012466082323 0.7894 -+- +rs12791593 t c 0.009550786888 0.015839807737 0.5465 +++ +rs3770636 t g 0.076380480708 0.066089248858 0.2478 -++ +rs605714 t c -0.009172003008 0.012984223109 0.4799 --- +rs6483189 t g -0.008609352417 0.019546960886 0.6596 --- +rs16855448 a t 0.012000000000 0.122000000000 0.9216 ??+ +rs831019 t g 0.007366304984 0.016016290496 0.6456 +++ +rs527788 a g 0.012328822207 0.013523202234 0.3619 ++- +rs4753436 a g -0.002220314582 0.013804786217 0.8722 --+ +rs522479 t c -0.015890392314 0.014114564914 0.2602 --+ +rs16856436 t g -0.000518780507 0.016028139640 0.9742 -+- +rs7949734 t g -0.006349396839 0.014029527003 0.6509 +-- +rs2605585 t c 0.006788310771 0.016533484555 0.6814 +++ +rs12577228 t c -0.012946745788 0.022200973135 0.5598 --+ +rs3843327 c g 0.007446729428 0.014262803366 0.6016 ++- +rs12421052 a t -0.025068081028 0.022077213135 0.2562 --+ +rs700552 c g -0.015227587149 0.014216206633 0.2841 +-- +rs11768656 t c 0.121200000000 0.176100000000 0.4913 +?? +rs16855373 c g 0.135600000000 0.109000000000 0.2135 +?? +rs3020066 c g -0.001644641292 0.014302553271 0.9085 +-+ +rs2331003 a g 0.011193447756 0.017880514492 0.5313 -++ +rs4642534 t c -0.011879438752 0.014164896919 0.4017 --- +rs498007 a c -0.015593202492 0.013082640295 0.2333 --+ +rs13419326 a c -0.064220000000 0.145300000000 0.6585 -?? +rs741038 a g 0.021646453024 0.015447577448 0.1611 -++ +rs2730613 a c -0.002377695975 0.013961540555 0.8648 -++ +rs534310 t c 0.021654841323 0.018265486141 0.2358 -++ +rs1181600 t c -0.017242491244 0.016116455221 0.2847 --- +rs4724254 t c 0.011878397632 0.017950308980 0.5081 +++ +rs726873 t c 0.011847901989 0.017943336708 0.5091 +++ +rs17267869 t c 0.083773585493 0.027975322693 0.002748 ++? +rs1863147 t g -0.000829422589 0.016374881409 0.9596 ++- +rs4668123 t c 0.018709956737 0.013378859420 0.162 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b/tests/test_10/metal.txt new file mode 100755 index 0000000..3d5ad3f --- /dev/null +++ b/tests/test_10/metal.txt @@ -0,0 +1,68 @@ +# This file includes a series of comments. Each comment is marked +# by a # character as the first character in the line. +# +# This is a comment! + +# Meta-analysis weighted by standard error does not work well +# when different studies used very different transformations. +# In this case, some attempt was made to use similar trait +# transformation and you can request a standard error based +# analysis by uncommenting the following line: +SCHEME STDERR + +# Usually, it is a good to apply genomic control to each +# input file. However, in this example, all the markers being +# examined reside in strongly associated loci and it probably +# is not a good idea. To find out what happens if you turn +# on genomic control, uncomment the following line. +# GENOMICCONTROL ON + +# To help identify allele flips, it can be useful to track +# allele frequencies in the meta-analysis. To enable this +# capability, uncomment the following two lines. +# AVERAGEFREQ ON +# MINMAXFREQ ON + +# To restric meta-analysis to two previously reported SNPs +# and summarize study specific results, uncomment the two +# lines that follow. +# ADDFILTER SNP IN (rs10830963,rs563694) +# VERBOSE ON + +# Describe and process the DGI input files +MARKER SNP +WEIGHT N +ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE +FREQ EFFECT_ALLELE_FREQ +EFFECT BETA +STDERR SE +PVAL P_VAL + +PROCESS ../Data/DGI_three_regions.txt + +# Describe and process the FUSION input files +MARKER SNP +ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE +FREQ FREQ_EFFECT +WEIGHT N +EFFECT BETA +STDERR SE +PVAL PVALUE + +PROCESS ../Data/MAGIC_FUSION_Results.txt.gz + +# Describe and process the SardiNIA input files +MARKER SNP +DEFAULT 4106 +ALLELE AL1 AL2 +FREQ FREQ1 +EFFECT EFFECT +STDERR SE +PVAL PVALUE + +PROCESS ../Data/magic_SARDINIA.tbl + +# Execute meta-analysis +EFFECT_PRINT_PRECISION 12 +STDERR_PRINT_PRECISION 12 +ANALYZE diff --git a/version/VersionInfo.h b/version/VersionInfo.h index 2d89c56..701cb7d 100644 --- a/version/VersionInfo.h +++ b/version/VersionInfo.h @@ -3,7 +3,7 @@ #ifndef VERSION -#define VERSION "2018-08-28" +#define VERSION "2020-05-05" #endif