[Genabel-commits] r1720 - in branches/ProbABEL-pvals/ProbABEL: . src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 30 16:50:58 CEST 2014
Author: lckarssen
Date: 2014-04-30 16:50:58 +0200 (Wed, 30 Apr 2014)
New Revision: 1720
Modified:
branches/ProbABEL-pvals/ProbABEL/configure.ac
branches/ProbABEL-pvals/ProbABEL/src/main.cpp
branches/ProbABEL-pvals/ProbABEL/src/main_functions_dump.cpp
Log:
ProbABEL p-vals branch:
- Changed WITH_BOOST preprocessor variable name to WITH_BOOST_MATH so we can later also separately check for other parts of the Boost library if necessary.
- Minor updates to the Doxygen documentation.
Modified: branches/ProbABEL-pvals/ProbABEL/configure.ac
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/configure.ac 2014-04-30 14:03:05 UTC (rev 1719)
+++ branches/ProbABEL-pvals/ProbABEL/configure.ac 2014-04-30 14:50:58 UTC (rev 1720)
@@ -39,7 +39,7 @@
# User did not set CPPFLAGS, so we can put in our own defaults
CPPFLAGS="-Wall"
fi
- CXXFLAGS+=" -g -Wextra"
+ CXXFLAGS+=" -g"
fi
if test "x$devoptions" = "xno"; then
@@ -91,9 +91,9 @@
fi
-# See if we can use the Boost libraries for calculating p-values
-AC_ARG_WITH([boost],
- AS_HELP_STRING([--with-boost], [Use the Boost Math library for
+# See if we can use the Boost math libraries for calculating p-values
+AC_ARG_WITH([boost-math],
+ AS_HELP_STRING([--with-boost-math], [Use the Boost Math library for
calculating p-values. This is enabled by default]
)
)
@@ -103,7 +103,7 @@
AC_ARG_WITH([boost-include-path],
[AS_HELP_STRING([--with-boost-include-path],
- [location of the Boost Math headers, defaults to /usr/include/boost])],
+ [location of the Boost headers, defaults to /usr/include/boost])],
[CXXFLAGS+=" -I${withval}"
CPPFLAGS+=" -I${withval}"],
[CXXFLAGS+=' -I/usr/include/boost'
@@ -118,10 +118,10 @@
to disable the calculation of p-values.])
fi
else
- AC_MSG_NOTICE([not using the Boost libraries, so no p-values in the \
+ AC_MSG_NOTICE([not using the Boost Math libraries, so no p-values in the \
output])
fi
-AM_CONDITIONAL([WITH_BOOST], test "x$with_boost" != "xno")
+AM_CONDITIONAL([WITH_BOOST_MATH], test "x$with_boost" != "xno")
# Checks for typedefs, structures, and compiler characteristics.
Modified: branches/ProbABEL-pvals/ProbABEL/src/main.cpp
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/src/main.cpp 2014-04-30 14:03:05 UTC (rev 1719)
+++ branches/ProbABEL-pvals/ProbABEL/src/main.cpp 2014-04-30 14:50:58 UTC (rev 1720)
@@ -242,7 +242,7 @@
std::vector<std::ostringstream *> covvalue;
std::vector<double*> chi2val; // vector that contains the chi2 values
std::vector<std::ostringstream *> chi2;
-#if WITH_BOOST
+#if WITH_BOOST_MATH
std::vector<std::ostringstream *> pval;
#endif
@@ -263,7 +263,7 @@
chi2[i]->precision(6);
// *chi2[i] << scientific;
chi2val.push_back(new double);
-#if WITH_BOOST
+#if WITH_BOOST_MATH
pval.push_back(new std::ostringstream());
pval[i]->precision(6);
#endif
@@ -559,7 +559,7 @@
} // END ngpreds == 1 (and SNP is rare)
} // END else: SNP is rare
-#if WITH_BOOST
+#if WITH_BOOST_MATH
// Calulate p-values based on the chi^2 values
int chi2df = 1;
*pval[model] << pchisq(*chi2val[model], chi2df);
@@ -583,7 +583,7 @@
#endif
*outfile[model] << chi2[model]->str();
-#if WITH_BOOST
+#if WITH_BOOST_MATH
*outfile[model] << input_var.getSep() << pval[model]->str();
#endif
@@ -601,7 +601,7 @@
#endif
*outfile[0] << chi2[0]->str();
-#if WITH_BOOST
+#if WITH_BOOST_MATH
*outfile[0] << input_var.getSep() << pval[0]->str();
#endif
@@ -616,7 +616,7 @@
covvalue[model]->str("");
// Oct 26, 2009
chi2[model]->str("");
-#if WITH_BOOST
+#if WITH_BOOST_MATH
pval[model]->str("");
#endif
}
@@ -663,7 +663,7 @@
++it;
}
-#if WITH_BOOST
+#if WITH_BOOST_MATH
it = pval.begin();
while (it != pval.end())
{
Modified: branches/ProbABEL-pvals/ProbABEL/src/main_functions_dump.cpp
===================================================================
--- branches/ProbABEL-pvals/ProbABEL/src/main_functions_dump.cpp 2014-04-30 14:03:05 UTC (rev 1719)
+++ branches/ProbABEL-pvals/ProbABEL/src/main_functions_dump.cpp 2014-04-30 14:50:58 UTC (rev 1720)
@@ -1,3 +1,12 @@
+/**
+ * \file main_functions_dump.cpp
+ * \author Yurii S. Aulchenko
+ * \author M. Kooyman
+ * \author L.C. Karssen
+ * \author Maksim V. Struchalin
+ *
+ * \brief File containing a bunch of functions used in main().
+ */
/*
* main_functions_dump.cpp
*
@@ -35,7 +44,7 @@
#include <iomanip>
#include <vector>
-#if WITH_BOOST
+#if WITH_BOOST_MATH
#include <boost/math/distributions.hpp>
#endif
@@ -263,7 +272,7 @@
#endif
}
*outfile[0] << input_var.getSep() << "chi2_SNP_add";
-#if WITH_BOOST
+#if WITH_BOOST_MATH
*outfile[0] << input_var.getSep() << "pval_SNP_add";
#endif
*outfile[0] << "\n";
@@ -350,7 +359,7 @@
*outfile[3] << input_var.getSep() << "chi2_SNP_rec";
*outfile[4] << input_var.getSep() << "chi2_SNP_odom";
-#ifdef WITH_BOOST
+#ifdef WITH_BOOST_MATH
*outfile[0] << input_var.getSep() << "pval_SNP_2df";
*outfile[1] << input_var.getSep() << "pval_SNP_add";
*outfile[2] << input_var.getSep() << "pval_SNP_dom";
@@ -372,7 +381,8 @@
/**
- * Write the information from the mlinfo file to the output file(s).
+ * \brief Write the information from the mlinfo file to the output
+ * file(s).
*
* \param outfile Vector of output file(s)
* \param file index number identifying the file in the vector of files
@@ -468,13 +478,16 @@
}
-#ifdef WITH_BOOST
+#if WITH_BOOST_MATH
/**
- * Calculate the p-value based on the chi^2 distribution.
+ * \brief Calculate the p-value based on the chi^2 distribution.
*
- * \param chi2 chi^2 value for which the p-value should be
+ * This function is only available if ./configure has detected the
+ * Boost Math libraries.
+ *
+ * \param chi2 \f$\chi^2\f$ value for which the \f$p\f$-value should be
* calculated.
- * \param df degrees of freedom of the chi^2 distribution
+ * \param df degrees of freedom of the \f$\chi^2\f$ distribution
*/
double pchisq(const double chi2, const int df)
{
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