CNIRRatio::CNIRRatio( std::shared_ptr< const CSeries > const& t_SolarRadiation,
double const lowLambda, double const highLambda ) {
auto integratedSolar = t_SolarRadiation->integrate( IntegrationType::Trapezoidal );
auto aSolarRange = CWavelengthRange( WavelengthRange::Solar );
auto totSolar = integratedSolar->sum( aSolarRange.minLambda(), aSolarRange.maxLambda() );
auto totVisible = integratedSolar->sum( lowLambda, highLambda );
m_Ratio = totVisible / totSolar;
}
/**
* Run multiple test.
*
* @param transaction_file The file includes associations between TFs and genes.
* Each line indicates a gene.
* If gene is targeted by the TF, then value is 1, otherwise 0.
* @param flag_file Each line indicates a gene. The column1 is gene name.
* If gene has the feature, the column2 is 1. The other case 0.
* @param threshold The statistical significance threshold.
* @param set_method The procedure name for calibration p-value (fisher/u_test/chi).
* @param max_comb the maximal size which the largest combination size in tests set.
* @param log_file File name for logging.
* @param alternative hypothesis, 1 -> greater, 0 -> two sided, -1 -> less
*/
void LampCore::run(std::string& transaction_file, std::string& flag_file, double threshold,
std::string& set_method, int max_comb,
std::string& log_file, int alternative) {
clean();
// read 2 files and get transaction list
std::cerr << "Read input files ..."<< std::endl;
try {
readFile.readFiles(transaction_file, flag_file, ',');
// If the alternative hypothesis is 'less',
// the positive and negative of observe values are reversed,
// and conduct the identical procedure to 'greater'.
if (alternative < 0)
reverseValue( readFile.getTransaction_list(), set_method );
if ((int)readFile.getColumnid2name().size() <= max_comb)
max_comb = -1;
} catch (std::string &msg) {
throw msg;
} catch (...) {
throw std::string("Error: An unexpected error occurred while trying to read input files.");
}
// run multiple test
std::string transaction4lcm53 = transaction_file + ".4lcm53";
// run
try {
FILE* fp_log = fopen(log_file.c_str(), "w");
if (fp_log == NULL)
throw std::string("Can't open file : " + log_file);
boost::iostreams::stream<boost::iostreams::file_descriptor_sink> outlog;
#if (BOOST_VERSION >= 104900)
outlog.open(fileno(fp_log), boost::iostreams::close_handle);
#else
outlog.open(fileno(fp_log), true);
#endif
starttime = std::chrono::high_resolution_clock::now();
std::cerr << "Compute the optimal correction factor ...";
double max_lambda = maxLambda(readFile.getTransaction_list());
fre_pattern = new LCM(max_lambda, fileno(fp_log));
lam_star = runMultTest(readFile.getTransaction_list(), transaction4lcm53,
threshold, set_method, max_comb, outlog, alternative,
max_lambda);
correction_term_time = std::chrono::high_resolution_clock::now();
k = fre_pattern->getTotal( lam_star );
std::cerr << " " << k << std::endl;
std::cerr << "Compute P-values of testable combinations ..." << std::endl;
fwerControll(max_lambda, threshold, outlog);
finish_test_time = std::chrono::high_resolution_clock::now();
outlog.close();
std::cerr << "Output results ..." << std::endl;
// If the positives and negatives are reversed, the number of positives is calculated.
if (( alternative < 0 ) && (std::find(BINARY_METHODS.begin(), BINARY_METHODS.end(), set_method) != BINARY_METHODS.end())) {
for (enrich_t* l : enrich_lst) {
l->stat_score = l->len - l->stat_score;
}
}
} catch (std::string &msg) {
throw msg;
} catch (...) {
throw std::string("Error: An unexpected error occurred while trying to test.");
}
}
