moseleybioinformaticslab/chi2plookup

chi2plookup package provides a simple interface for creating C++ header file that contains pre-generated array(s) of p-values for chi-square distribution.

chi2plookup

The chi2plookup package provides a simple interface for creating C++ header file for use in C++ projects. This header file contains pregenerated array(s) of p-values for chi-square distribution for specified degrees of freedom.

Why?

Need a way to calculate p-value for different degrees of freedom for a given chi2 value and bypass third-party dependencies:

• boost
• gsl (GNU Scientific Library)

Inspired by:

• http://rmflight.github.io/posts/2013/10/precalcLookup.html
• https://stackoverflow.com/questions/795972/chi-squared-probability-function-in-c

Usage example

1. To view command-line help message:

$ python3 -m chi2plookup --help

chi2plookup command-line interface

Usage:
    chi2plookup -h | --help
    chi2plookup --version
    chi2plookup generate [--headerfile=<path>] [--precision=<precision>] [--df=<df>] [--start_chi=<start_chi>] [--verbose]

Options:
    -h, --help                    Show this screen.
    --version                     Show version.
    --verbose                     Print more information.
    --headerfile=<path>           Path where to save generated header file [default: Chi2PLookup.h]
    --precision=<precision>       Parameter that controls precision [default: 10000].
    --df=<df>                     Degrees of freedom, how many to ganarate [default: 6].
    --start_chi=<start_chi>       Maximum chi2 value for given degree of freedom [default: 25].

2. Generate a header file with p-values for necessary degrees of freedom (we are using default number degrees of freedom, precision, and header file path):

$ python3 -m chi2plookup generate --verbose

Generating p-value arrays...
  df=6
  precision=10000

    Adding p-values array to template for degree of freedom = 1 ...
    Adding p-values array to template for degree of freedom = 2 ...
    Adding p-values array to template for degree of freedom = 3 ...
    Adding p-values array to template for degree of freedom = 4 ...
    Adding p-values array to template for degree of freedom = 5 ...
    Adding p-values array to template for degree of freedom = 6 ...

3. Use generated file within your C++ project.

#include <iostream>
#include "Chi2PLookup.h"

int main() {

    Chi2PLookup Chi2PLookupTable;
    double x = 1;
    int df = 1;
    double outvalue;

    outvalue = Chi2PLookupTable.getPValue(x, df);
    std::cout << outvalue << "\n";

    return 0;
}

Note

Use the following approach for smaller number of degrees of freedom to avoid generating huge header files (e.g. header file with 6 degrees of freedom ~34 MB).